<File 'try31807_30004_Xba.brlmm.cn.wig' - track load error:
Limit of 10,000,000 length specification for bed format at line 1, found: 69250877>
This error message is a result of certain restrictions that UCSC has for its online genome browser. This particular restriction requires that no segment spans a distance greater than 10,000,000 base pairs on a chromosome.
Unfortunately, we are unable to adapt our algorithm to the UCSC Genome browser requirements, but we do however, have two workarounds for this issue:
1. The first workaround is to increase the maximum pairwise permuted p-value in the copy number segmenting options. Increasing the maximum allowable p-value will result in the data being divided into a greater number of segments.
However, this option has a number of disadvantages. First, this workaround will require some trial and error to find a p-value that will generate allowable results in the UCSC online genome browser. Secondly, increasing your acceptable p-value may have an effect on your overall analysis by increasing the likelihood of finding insignificant segments.
If you would like to take this route, note you may need to increase the max segments per window parameter as the analysis will result in more found segments. Also, you may want to increase the minimum number of SNPs per segment to a number greater than one because the online genome browser will also return an error if a segment of length one is found (which is more likely with multivariate analysis). Feel free to contact the group at UCSC with questions about the genome browser (genome@soe.ucsc.edu).They are usually very helpful when answering questions.
2. The second workaround is usually more effective. Affymetrix has a genome browser tool, Affymetrix IGB, available for free download. This genome browser will accept UCSC Wiggle files, as well as a number of other data types, including Affymetrix annotations files. Because the genome browser is installed and run on your local computer, it does not enforce restrictions on your data. To run IGB, you will need to have installed Java Web Start. Find information about IGB and Java Web Start at the following site:
http://www.affymetrix.com/support/developer/tools/download_igb.affx
From that site you can launch Affymetrix IGB, which will automatically install it on your computer.
Affymetrix IGB is often preferable to the UCSC online genome browser because it does not require that you tailor your analysis according to UCSC's capabilities.We have also found IGB more user friendly due to added control over the plot appearance.
