Gene expression comparison

[Constructor]

Good day everyone.

First of all, I must admit, that I’m completely newbie it this area, so forgive me for some stupid questions, if there ll be.

My goal is to compare expression of different genes, using data from http://genome.ucsc.edu/ and our experimental values. As I understand by the moment – Ill have to compare something like wig files, to find out from them information for each gene (from the information for each position) and then to compare this data.

So, if someone will give me a piece of advice which programs and R packages I should check – it would be great.

Thx for your time

[dpryan]

I imagine it would be more straight forward to just download the original BAM (or other alignment format, or even the raw reads and then align them yourself) alignments from GEO or whatever and then use HTSeq-count and DESeq (or whatever). Trying to use the wig files seems suboptimal.

[Constructor]

Thx. Ill try it.