‹‹ Back to SVS Home

Importing Data

4.3 Importing Data

The File->Import Data submenu presents various menu items for importing different types of data:

1. Import Wizard
2. Import ASCII File
3. Import Family-Based Data
4. Import Legacy GHD File
5. Import DSF File
6. Import Genetic Marker Map
7. Import Affymetrix CHP Files
8. Import PED/BED File

These methods for importing data are described in the following sections.

4.3.1 The Import Wizard

---

---

To open the Import Wizard, select the File->Import Data->Import Wizard menu item from the HelixTree main menu. The Import Wizard is shown in Fig. 4.2 The Import Wizard allows you to specify the source of your data which can either be one of the file types listed in the following table or an ODBC data source. Note that some of the file formats may not be available on your operating system. Also, unless otherwise noted, the Import Wizard can import all versions of the specified file format.

File Type	Version Information	File extension(s)
1-2-3	All versions of 1-2-3 can be read.	*.wk*, *.wr*
Access		*.mdb
ASCII - Delimited		*.txt, *.csv
ASCII- Fixed Format		*.sts
dBASE, Foxpro, Clipper, and Alpha Four and compatible formats	All versions can be read.	*.dbf
Epi Info	All versions can be read.	*.rec
Excel	All versions of Microsoft Excel files through the Excel 2000 can be read.	*.xls
Gauss		*.dat
JMP		*.jmp
LIMDEP		*.lpj
Matlab Matrices		*.mat
Mineset		*.schema, *.sch
Minitab	All versions through version twelve can be read.	*.mtw
ODBC		requires ODBC driver and Data Source Name (DSN)
OSIRIS		*.dct, *.dict
Paradox	All versions through version seven can be read.	*.db
Quattro Pro		*.wq?, *.wb?
SAS Data Files	Versions 6 through 9 can be read.	*.sd2, *.ssd01, *.ssd04, *sd7, *.sas7bdat, *.sav, *.por
SAS Transport Files		*.xpt, *.tpt
S-PLUS	All versions of S-Plus matrices, lists and dataframes can be read.	*.
SPSS Data		*.sav
SPSS Portable		*.por
Stata		*.dta
Statistica	All versions through version five.	*.sta
SYSTAT		*.sys

4.3.1.1 Importing Files

In order to specify a file for importing, you must left click the File button. This will cause the Open dialog to be displayed which allows you to navigate through your file system and select the file to be imported. The Open dialog has a drop down control with the label Files of type. Use this control to specify the specific file type that you are importing. Once you have selected the file and specified its type, left click the Open button to return to the Import Wizard.

The Name and Format controls displayed on the first panel of the Import Wizard are "read only". So, you will not be able to directly type in information about the file you want to import. However, once you have used the Open dialog to select a file for importing, the Name and Format controls will be filled in with correct information.

If your file contains genetic data, you will need to specify the character that is used to delimit alleles. By left clicking on the Allele delimiter drop down control, you will be able to choose one of four possible characters as the delimiter: underscore ’_’, forward slash ’/’, comma ’,’, and space ’ ’.

---

---

Left click the Next button to view the second panel of the Import Wizard which is shown in Fig. 4.3. This panel allows you to identify the label column. The label column contains information (labels) that identify each row of data. The label column is not used during analysis, but the labels are used in several graphs produced by HelixTree.

By default, the Import Wizard assumes that there is no label column. However if your data set does contain a label column, left click on the Select label column radio button and highlight the name of the column that contains the label data. When you have completed your selection, left click on the Finish button to dismiss the Import Wizard and return to the HelixTree main window. A new dataset will have been added to the Navigator Window and a new spreadsheet will be opened up for viewing the data.

4.3.1.2 Importing ODBC Data

---

---

If the data that you want to import is accessible via an ODBC data source name (DSN), you must left click the ODBC Driver button shown on the first panel of the Import Wizard (see Fig. 4.2). This will result in the display of the ODBC Data Sources dialog which displays all the known DSNs (see Fig. 4.4). Select the DSN that you would like to import and click the Use Data Source button. You will be returned to the first panel of the Import Wizard where you will see the Source and Driver text controls filled in with the name of the data source and driver you have chosen.

If your file contains genetic data, you will need to specify the character that is used to delimit alleles. By left clicking on the Allele delimiter drop down control, you will be able to choose one of four possible characters as the delimiter: underscore ’_’, forward slash ’/’, comma ’,’, and space ’ ’.

Once you have identified the Allele delimiter left click the Next button. What happens after this depends entirely upon the type of DSN you have selected. For our purposes we can say that there are two categories of DSNs. Those that identify resources native to Microsoft Windows such as Microsoft Access databases and those that identify non-native resources such as Oracle or MySQL databases. Even within these two categories, there are variations on what happens next that depend on the specific resource.

If your DSN represents a resource native to Microsoft Windows such as a Microsoft Access database, you will be shown the second panel of the Import Wizard. This panel will allow you to choose the specific resource that you want to import. For instance, you could identify a particular Microsoft Access database. Once you have made your selection, click the Next button to view the third panel of the Import Wizard. You will then be asked to identify the specific table or file to be imported. Once you have made your selection, click the Next button to view the fourth panel of the Import Wizard. At this point you will be asked to identify a label column if there is one. Clicking the Finish button will cause the data source to be imported, the Import Wizard to be closed and a Spread Sheet Viewer to be displayed with the imported data.

If your DSN represents a resource not native to Microsoft Windows such as an Oracle or MySQL database, you will be shown a dialog box external to the Import Wizard that was provided by the vendor of the ODBC driver. The vendor dialog will ask you to provide the host, server name or IP address of the computer hosting the data source, the port number of the database server and the user ID and password. All of this information is used by the ODBC driver to establish a connection to the DSN. Once the vendor dialog box is dismissed, a connection will be established and you will be returned to the Import Wizard. You will then navigate through the Import Wizard panels identifying the specific table and label column as was described above for native resources.

4.3.2 Importing ASCII Data Files

Although the import wizard enables the import of non-family-based ASCII files, HelixTree also provides a separate utility for the conversion of these files. From within a HelixTree project’s main screen select the menu choice File->Import Data->Import ASCII file.

---

---

---

---

From this subsequent dialog you need to identify an ASCII source file, select how the file is delimited and what column, if any, holds row labels.

First click on the Choose… button to open a typical file-find dialog. Navigate to the HelixTree\example folder. Located here are the sample files included with HelixTree. We use a CSV extension to indicate comma delimited files and DAT to indicate space delimited. After selecting a file click Open to continue.

---

---

If you are getting files from other sources things may not be so neat. Many applications that export these structured files give them a TXT extension. See the section File Formats for a description of how these files are structured. For clarity you may want to rename your file’s extension to conform to this protocol.

---

---

Since we picked a CSV file we need to change the File format: pull-down to indicate the file is Comma delimited.

If the data has a single field that identifies each record, you can indicate this in the row Label column number: text box. For example, the data set above has a patient id and it is the first field in the left-to-right sequence of fields. The label column is for identification only and is not used for data analysis.

---

---

On a very large data set the importation process may take some time. There is a progress indicator (not shown) that helps estimate your progress.

Once the data has been converted you will see a summary of the processing. This should match your expectations of data types and number of records. Dismiss by clicking the OK button.

When finished you are returned to the main navigation screen of HelixTree where you will see a new icon for the imported data and a new icon for a spreadsheet containing the imported data. The spreadsheet is automatically opened and ready for further analysis.

---

---

4.3.3 Importing Legacy GHD Files

Users of HelixTree prior to release 3.0 may have data files already in the GHD format. In fact, some of the files included in the examples directory are stored in legacy format. In order to continue to be used, these legacy files need to be imported into a project. This is done by selecting the File->Import Data->Import legacy GHD File menu item. An Open dialog is displayed which allows you to navigate to the folder where the GHD file is located. Selecting the GHD file and clicking on the Open button will cause the file to be imported, the Open dialog to be closed and control to be returned to the HelixTree main window. The imported GHD file is automatically added to the current project and displayed in a Spread Sheet Viewer. Fig. 4.11 shows the legacy GHD data file, data_312.ghd, being selected for import. As you can see, data_312.ghd is located in the example folder. It contains simulated genetics data with one dependent variable labeled Response.

---

---

4.3.4 Importing DSF Files

Many users have noticed that HelixTree stores data in a very efficient and compact format. The Dataset Storage Format (DSF) is designed to allow for the sharing and collaboration of data sets between HelixTree users. The DSF format is also open to third-parties to develop the ability to create DSF files from their own products or data sources and thus more easily integrate with HelixTree. To import a DSF file generated by an external source or exported from HelixTree’s Spreadsheet Menu (see 6.3.3), select the File->Import Data->Import DSF File menu item.

An Open dialog is displayed which allows you to navigate to the folder where the DSF file is located. Selecting the DSF file and clicking on the Open button will cause the file to be imported, the Open dialog to be closed and control to be returned to the HelixTree main window. The imported data is automatically added to the current project and displayed in a Spread Sheet Viewer.

4.3.5 Importing Genetic Marker Maps

4.3.5.1 Importing Genetic Marker Maps Overview

Genetic marker maps contain distance data for individual SNPs relative to some origin, as well as other data relative to the SNPs.

Although it is possible, normally HelixTree is not used to analyze the genetic marker map data in its own right. Rather, the genetic marker map data is associated with one or more data files which contain genetic marker data that are actually being studied. Frequently, a team of analysts will have one master genetic marker map that is used with all analysis projects.

Genetic marker map files must be ASCII files that contain tabular data with the values separated by commas, spaces or tabs. For retrieving genetic marker maps directly from the Affymetrix NetAffx service, see section 4.3.5.3. The first row must contain the labels for the columns.

At a bare minimum, there must be two columns in the genetic marker map. There must be columns that contain:

1. the identifiers for the genetic markers, and
2. the distance data (absolute within the current chromosome).

Optionally, the genetic marker map can contain four additional columns in any combination. These columns contain:

1. the identity of the chromosome where the SNP is located,
2. a region within the chromosome where the SNP is located,
3. an RS ID for the SNP, and
4. the name (if known) of a gene containing the SNP.

A marker map may be “applied” to a spreadsheet containing genetic marker data. This will create a resulting spreadsheet whose columns are sorted according to first, chromosome, and second, distance. In addition, marker map information will be invisibly stored within the columns of the resulting spreadsheet.

Additional features are available from marker-mapped spreadsheets. These include:

1. Activating/inactivating columns by chromosome, region, and/or gene.
2. Plotting LD or HWE with the data spaced according to distance (with gaps placed at chromosome boundaries). To access this, use the menu and choose the first LD or the first HWE option, rather than the second one which says “(uniform distances)”.
3. In trees derived from mapped spreadsheets, the Haplotype Trend Regression option allows you to specify a window according to genetic distance. (Such a window will be cut short if it would otherwise cross a chromosome boundary.)

NOTE: The current marker map sort order (for versions of HelixTree on or after release 4.4.2) is, as stated above, chromosome and distance.

NOTE: Versions of HelixTree on or after release 4.3.0 and before release 4.4.2 sorted marker maps, and their mapped spreadsheet columns, according to chromosome, region name, gene name, and finally distance.

NOTE: Versions of HelixTree before release 4.3.0 sorted marker maps according to chromosome, region name, and distance.

NOTE: Versions of HelixTree on or before release 3.1.0 left the columns of the resulting spreadsheet in the same order as the original spreadsheet. Their maps, however, were still considered to be sorted (by chromosome, region name, and distance).

4.3.5.2 Importing A Genetic Marker Map

The process of importing a genetic marker map begins by selecting the File->Import Data->Import Genetic Marker Map menu item. Selecting this menu option will display a dialog for choosing the marker map (see Fig. 4.12).

---

---

Clicking the Choose button will cause a standard file Open dialog to be displayed (see Fig. 4.13). Note that we have selected a map file data_312.map from the example directory.

Note: typically Affymetrix marker maps are obtained by exporting annotations as a tab-delimited text (*.TXT) file from GDAS. In the current version of GDAS, there is an extra row added at the top of the file in addition to the column labels that needs to be ignored. For these files, check the box that reads “Ignore the first line of the file”.

---

---

Once you have selected the map file, clicking the Open button will return us to the dialog for choosing the marker map (see Fig. 4.14). At this point the Input ASCII map file text field now contains the name of the selected file. We must also set the file format. We have selected comma delimited from the drop down menu. After both fields are set, click the OK button to display the Select Marker Map Columns Dialog (see Fig. 4.15).

---

---

---

---

The Select Marker Map Columns dialog contains six drop down controls. Each control, when selected, will display all of the column headers in the marker map allowing you to associate a specific column with the appropriate marker map data. For instance, the data_312.map has a Name column which contains the SNP/Marker IDs. It also has a Dist column which contains all of the distance information, as well as columns corresponding to all of the other marker map fields. Fig. 4.16 shows all of the drop down controls filled in with the appropriate column headers from the data_312.map file.

---

---

Clicking the OK button dismisses the Select Marker Map Columns dialog and causes a Marker Map Import summary message box to be displayed (see Fig. 4.17). Click OK to continue.

---

---

Clicking the OK button dismisses the Marker Map Import summary message box and causes a spread sheet viewer to be displayed with the imported data (see Fig. 4.18). You now also see two new nodes in the Project Navigator window. One node represents the marker map as a data set and the other node represents the corresponding spread sheet viewer.

---

---

4.3.5.3 Importing a Genetic Marker Map Using Affymetrix NetAffx

---

---

Affymetrix NetAffx^TM provides array design and annotation information for their GeneChip^TM array results. Through their website at http://www.affymetrix.com/ you can sign up for and use the NetAffx^TM Analysis Center.

HelixTree is able to communicate with the NetAffx^TM through a web service interface allowing the user to download and update genetic marker map information that can be mapped to data imported from Affymetrix CHP files (See section 4.3.6 for importing CHP files).

To import genetic marker map information from the Affymetrix NetAffx^TM service, select the File->Import Data->Download Affymetrix Marker Map menu item from the HelixTree main menu.

You will be prompted for login credentials for the NetAffx^TM service. Login credentials can be freely obtained through registering on Affymetrix’s website.

NOTE:If your internet connection goes through a proxy which requires authentication, HelixTree may not be able to communicate with the Affymetrix NetAffx service. Strict firewalls may also preclude communication with NetAffx.

---

---

Once authenticated, HelixTree will load the latest annotation listings and place them in the files list on the upper half of the dialog. Previously downloaded marker map files will be listed in the bottom half of the dialog.

Select one or more annotation files in the top listing and click Download to download, combine and sort the annotation listing into a map file. If Import into project when downloaded is checked, the map file will be loaded automatically into the currently opened project.

Note that the 50K and 250K annotation files come in pairs. For example, be sure to select both Mapping50K_Hind240annot.csv and Mapping50K_Xba240annot.csv. Once downloaded, the annotations will show up in the Local Marker Map Files listing in later uses as Mapping50K_Hind240annot-Mapping50K_Xba240annot.map.

For convenience, all previously downloaded annotation files are listed in the bottom half of the dialog. Select one of these and click Load Into Project to import that marker map into the current project. You can also delete previously downloaded marker maps by selecting the corresponding item in the Local Marker Map Files list and clicking Delete File. Alternatively, you can manage these files manually by clicking View Directory (Under windows this will open an explorer window to the HelixTree marker maps directory. Under OS X and Linux a dialog containing the location of the directory will be displayed).

To delete a previously downloaded marker map, highlight the

4.3.5.4 Associating A Genetic Marker Map with a Data File

In order to use a marker map, it must be associated with a data file. To perform the association, both the marker map and the data file must already be imported into the same project. For illustration, we will use the legacy GHD file, data_312.ghd, as the data file and data_312.map as the marker map. To keep the illustration simple, all other nodes have been deleted from the project. Figure 4.21 shows the current state of the project as seen in the Project Navigator window.

---

---

Double click on the spread sheet viewer node for the data_312 data set to open the spread sheet viewer window. In Figure 4.21, the spread sheet viewer has an ID equal to 3. On the spread sheet viewer main menu, select the File->Apply Gene Marker Map menu item (see Figure 4.22) to display the Marker Map Chooser dialog box (see Figure 4.23).

---

---

---

---

In this dialog marker map spread sheets are highlighted in white, select the spread sheet viewer that contains the marker map that you want to associate with the data file. In Figure 4.23, the marker map spread sheet viewer has an ID equal to 6. Click the OK button to dismiss the Marker Map Chooser dialog box. An Apply Marker Map message box is displayed that summarizes the status of the mapping. Click the OK button to dismiss the Apply Marker Map message box. Once the message box is dismissed, a new spread sheet viewer is displayed called Marker Mapped Spreadsheet. The new spread sheet will have all the columns of the original data_312 data set spread sheet, however they will be reordered to match the marker map order for easier analysis. A node for the spread sheet viewer is also added to the Project Navigator (see Figure 4.24). The new spread sheet viewer contains the original data with distance information now mapped to it. The distance information is not visible in the spreadsheet as is the original data. Rather, it is managed by the spread sheet viewer as meta data and is made visible in certain types of analysis as previously mentioned. There are, however, script commands to view this information.

---

---

4.3.6 Importing Affymetrix CHP files

HelixTree is able to directly import Affymetrix 10k, 100k 500k, 5.0, and 6.0 GeneChip mapping array, "CHP" files.

4.3.6.1 Affymetrix Files Installation

For mapping arrays prior to the SNP 5.0 and SNP 6.0 arrays, you must have the corresponding library file installed for each type of mapping array you want to import. SNP 5.0 and 6.0 mapping arrays do not require library files. If you have GCOS installed, it is likely the library files are already installed in either C:/GeneChip/Library or C:/GeneChip/Affy_Data/Library.

To make life easier for non-GCOS users, we have provided a zip file containing the necessary subset of files needed for HelixTree. If you want the 10k and 100k mapping array library files. They can be found at:

http://www.goldenhelix.com/download/bin/Affy_LibraryFiles.zip.

This zip file should be unzipped to c:/GeneChip/Library (/home/GeneChip/Library for non-Windows).

To get the 10k, 100k, and 500k library files all together, you can retrieve them from:

http://www.goldenhelix.com/download/bin/Affy_10k50k250k_LibraryFiles.zip.

Again, this zip file should be unzipped to c:/GeneChip/Library (/home/GeneChip/Library for non-Windows).

It is also possible to download other Library files from Affymetrix through the NetAffx service. See section 4.3.8 for importing library files through NetAffx.

HelixTree will by default look for the mapping array library files in the GeneChip/Library directory, though it gives the option to choose another directory. For your convenience, it is recommended you save these library files to c:/GeneChip/Library (/home/GeneChip/Library for non-Windows).

These library files are for the final versions of these mapping arrays. If you were using an experimental early access array, you will need to get the appropriate library files from Affymetrix. All that is needed for HelixTree is the .CDF and .psi files for the array.

4.3.6.2 Affymetrix Mapping Array Import

To import Affymetrix CHP files, from the main HelixTree menu select the File->Import Data->Import Affymetrix CHP file menu item.

---

---

You will see the following dialog that enables you to specify the data that you wish to import.

---

---

Note, the “100k” and “500k” arrays, are respectively composed of two “50k” and two “250k” chips, with their respective library files. These need to be imported separately, and then joined together from the spreadsheet file menu, “Join Spreadsheets by Sorting”.

CHP files may be selected on a file-by-file basis, or by directory. To choose on a file-by-file basis, click Choose CHP Files and navigate to the location of your "CHP" files.

---

---

NOTE: This chooser will start at the stated location of the run-time libraries (see below).

After locating your CHP files, highlight the ones you want to import. In figure 4.27 we have selected a number of the files and their names are displayed in the File name text box. Click OK or OPEN to continue.

This brings us back to the original import window. The selected CHP files are displayed. From here, the list of selected CHP files can be managed. You have the option to select more files(by clicking Choose CHP Files or Add Directory), or remove files from the import list(by highlighting the files you wish to remove, and clicking Remove Selected Files).

Alternatively, if you would like to import all CHP Files in a directory, select Add Directory, navigate to the directory containing the CHP Files, and Click OK or OPEN. This will add the CHP Files contained in the directory to the list of selected files. Again, you now have the options to add or remove files from the list.

---

---

In the import window, the default location for library files of c:/GeneChip/Library is already filled in. If that is not correct click the Select button and choose the correct location of the run-time libraries. This location will be remembered with the project information. Installation instructions for the run-time libraries can be found in section 4.3.6. If you are importing SNP 5.0 or 6.0 arrays the library files location can be ignored, as it will not be needed for the import process.

If you wish to use a different threshold for the confidence score, tick the check-box and fill in the desired confidence score.

NOTE: Changing the confidence score is only valid for certain of the later file types such as 100K CHP files or 500K CHP files. During the import process, HelixTree will screen whether changing the confidence score is valid for your particular files.

You can optionally select a file that contains sample attribute information for the CHP files selected. The information parsed from these standard Affymetrix files (such as .ARR files exported from the GeneChip^TM Command Console) will be displayed in the annotations field of the imported data set.

Click Import to complete the process.

---

---

A display of the import statistics will show. After you press “OK”, a new spreadsheet will appear, and two new Navigator Nodes will appear in the Project Navigator panel–one for the data set and one for the spreadsheet that displays the data for selection and analysis.

Note, that Affymetrix CHP files do not contain phenotypic information or case/control information about the individuals. This data would have to be imported separately. When doing so, make sure that the label column for those individuals matches the CHP file identifier in the spreadsheet. Then, from either spreadsheet you can join on column labels to get a combined spreadsheet.

Note, also that you may wish to import marker map information for the mapping array data set. These can be exported as a tab-delimited text file from GDAS. Annotation data can also be retrieved from Affymetrix. With appropriate login privileges The 10k annotations CSV file can be downloaded from the “NetAffx Annotation Files” section of the following web page:

http://www.affymetrix.com/support/technical/byproduct.affx?product=10k

Likewise, annotation files can be downloaded for the 10k 2.0, 100k and 500k mapping arrays from:

http://www.affymetrix.com/support/technical/byproduct.affx?product=10k-20

http://www.affymetrix.com/support/technical/byproduct.affx?product=100k.

and

http://www.affymetrix.com/support/technical/byproduct.affx?product=500k.

The details of importing and applying a marker map can be found in section 4.3.5.

---

---

4.3.7 Import PED/BED File

Although you can import regular FBAT/PBAT pedigree files through the PBAT menu, PLINK has popularized a two file PED/MAP format that often contains both family-based and regular genotype data. HelixTree can import both the plain text PED/MAP files as well as the optimized binary PED or BED files (which should have correlating BIM/FAM files).

Because these files have full marker map information for each SNP, the marker map is also imported into HelixTree and you have the option of automatically creating a spreadsheet with that marker map applied. If you decide not apply a marker map, you can do so at a later time in the regular fashion.

4.3.7.1 Text PED/MAP File Import

---

---

In the import window for text PED/MAP files you can browse for your PED file by clicking the Browse button. The MAP file will be automatically filled in, but you may choose to browse for a different MAP file.

Leave the Create an Applied Marker Map Spreadsheet checked if you would like a spreadsheet created with the marker map defined in the MAP file applied. You can uncheck it for a slight performance gain.

The PLINK default is to encode missing phenotypes in the Sex or Affection Status column as “-9” and missing genotypes as “0”. If your PED file has a different encoding you can specify it in the Missing genotype and Missing phenotype fields.

NOTE: The first four columns of the PED file format are identifiers and encode missing values with the “0” string.

4.3.7.2 Binary BED/FAM/BIM File Import

---

---

The PLINK package also produces “Binary PED” files. The format consists of three files, with the extensions BED, FAM and BIM. The BED file stores compressed binary genotype information, the FAM file holds the pedigree/phenotype information (the first six columns of a text PED file) and the BIM file contains the information from a regular MAP file plus some additional allele information.

Once you select a BED file, the FAM and BIM file fields will be filled in with the logical corresponding names. You may of course browse to specify other files than the default assumptions. HelixTree only supports the default SNP-major mode of BED files, as the transposed individual-major mode is fairly unconventional. You can not specify custom missing value encoding for the binary format as the default missing values are assumed as they are in PLINK.

Of course you can still choose weather to create the marker mapped spreadsheet on import.

NOTE: The Binary BED/FAM/BIM import format is only available if you are licensed with the whole genome analysis feature.

4.3.8 Downloading Affymetrix Library Files Using the NetAffx Service

Through the Affymetrix NetAffx web service, HelixTree is able to download additional Affymetrix library files.

---

---

To download library files to use with HelixTree, select the Tools->Download Affymetrix Library File menu option from the main HelixTree window. You will be prompted for your Affymetrix NetAffx login information, which can be freely obtained by registering on Affymetrix’s website.

After entering your authentication information, HelixTree will load a list of library files available through the NetAffx service. These files will be displayed in the upper window of the download dialog. The lower window of the dialog will display all library files which have been previously downloaded and are contained in the HelixTree/AffyLibraryFiles directory.

To download library files, select one or more files from the upper window, and click Download. The file(s) will automatically be downloaded to the HelixTree/AffyLibraryFiles directory. When the desired files have been downloaded, they will appear in the lower window. If a newly downloaded file conflicts with an existing file, you will be prompted for whether or not to replace the existing file. Answering “Yes” will delete the old file, and replace it with the new file. Answering “No” will simply discard the newly downloaded file.

You can delete previously downloaded library files by selecting the corresponding item in the Local Affymetrix Library Files list and clicking Delete File. Alternatively, you can manage these files manually by clicking View Directory (Under windows this will open an explorer window to the HelixTree library files directory. Under OS X and Linux a dialog containing the location of the directory will be displayed).

Click Close to exit when finished.