Alt analyze question
Eugene Bolotin, PhD
I have a dataset from illumina bead arrays, unfortunately it is in a giant text file with about 1000 columns (experiments) and a row for each probeset. I analyzed it using limma R packge. I know the illumina array is not designed for this, but I would like to get alternate splcing data on genes with multiple probes in this array. Is there a way to do it with altanalyze? Can you reccomend any other softwares for the task?
Thanks,
Eugene
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Eugene Bolotin, Ph.D.
Genetics Genomics and Bioinformatics
Nathan Salomonis
This is now possible in the current version of AltAnalyze. I just
posted a page outlining how to do this on our wiki:
http://code.google.com/p/altanalyze/wiki/SplicingForAnyPlatform
The key is to reformat your data into a universally generic import
format (UCSC BED) and treat this data as if it is RNA-Seq expression
data. Instead of counts, you may have intensity data, which is fine. A
1000 columns is fine, but you will just want to make sure that you
create your groups and comparison file before running AltAnalyze as
described here:
http://code.google.com/p/altanalyze/wiki/ManualGroupsCompsCreation
I have not worked with non-Affy and non-RNA-Seq data yet, but there is
no reason I know of why this should work. Please contact me if you are
having problems with this.
Best,
Nathan Salomonis
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