161202 Struggling with DESeq2 - npslindstrom/DE-analysis GitHub Wiki

So today we had meeting in the project group. Linnea had found that the long-noncoding RNAs were already annotated as such in the FPKM-file we have recieved so we can use that to infer the EnsambleIDs of the relevant rows in the counts_table.txt.

We tried to run DESeq on the data but failed due to the terminal freezing over and over again.

Later during the day I tried to do it from my home computer, basically repeating part C of Lab3 but on the actual project data. It seemed to have worked fine.

My next step was to try to do the same thing using DESeq2 but quickly realized that DESeq2 does not use the same commands as DESeq1...

I thin I am getting a better understanding of R. I have been trying to write an R-script that can be called in R to do the analysis but it is difficult since all the commands have changed from DESeq1. So no good code to show so far, only a few tests, nothing substantial.