Analyzing Illumina Counts

I'm pretty new to all of this--forgive me if this is a simple question.

When I download illumina counts from GEO (like the supplementary file in GSE89225). Can I do comparisons directly on that file? Is there some normalization procedure I should go through?

Thanks!

• What type of comparison?
– arup
Aug 21 '17 at 17:11

For convenience, in DESeq2 you would want the DESeqDatasetFromMatrix() function after loading this.