Dear forum members :)
I'm a newb at R and bioinformatics so I am finding myself a little flustered by what to do now. I have obtained a gene expression matrix CPM normalized, with close to 15,000 genes and 16 total samples -> 4 samples in 4 groups. I have been trying to follow the pipelines directed in various packages but I always seem to get lost. So just a couple of questions for all of the great people out here:
1) I would like to get p and q values for the comparison groups as well as their fold changes. To get the fold change, can I just average their expression across 4 samples and apply log2(average(treatment)/average(control))? Can I just apply a t test to get the p values between groups, (when I do it the p values seem way to high)?
2) What kinds of tests can I do to check that my data is not skewed in any way i.e. overall check for integrity of the data?
3) I keep seeing TMM term being thrown around on the forum but I still can't see clearly what it means...
Thank you all so much. Any help is greatly appreciated :)