161201 The work begins - npslindstrom/DE-analysis GitHub Wiki

Today I have been looking at the data and reading a manual for using DESeq2 to analyze count data.

http://www.bioconductor.org/packages/2.13/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf

I am a bit confused at the moment regarding how to use it. I feel like my programming skills are severely lacking so learning a bit more of BASH and R seems like an natural next step. I will try to repeat the section of LAB3 that dealt with DESeq1 and see if I can parse some of the code we used there to try and understand how it can be adapted for our puposes.

It seems like DESeq2 needs the raw count data and not the normalized FPKM-values as we previously assumed. I feel like as soon as we can get DESeq up and running everything should be pretty smooth from there on.

Update: I think I understand the code used in LAB3 now. I am starting to feel like I can grasp what we are supposed to do better now. I want to try to use DESeq2 on our data to see if I can get it to work but I will wait until I can meet with the rest of the group so we can talk about data handling and security. I don't want to mess up the data by mistake since I am not sure if there are backups or not.