Dear R-gurus,
We have mRNA expression data that was generated by solexa-illumina deep
sequencing (75 nt reads), for two developmental stages, and we would
like to have genes that are differentially expressed, by using
procedures that were developed for microarrays, like samr, siggenes or
limma.
Counts for unique reads are normalized by gene length and also by the
total number of reads obtained for the library, followed by a log2
transformation.
My problem is that many genes have a count of 0, so taking the log is
not possible. The workaround I used is to add arbitrarily 1 to all the
counts before the log transformation.
1/ Does that sound ok to you guys?
2/ Does anyone knows a package that would deal directly with the counts
for the statistical analysis?
Thanks a lot,
Best regards,
-- Eric
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