I am so sorry to bother you all. I am new to microarrays/R.
Currently I am looking at gene expression patterns and have done ssn normalization and adjustments. I need to remove all genes that fail p value cut offs. My PI wants to use two different possible cut offs first to determine number of genes significant for either and go from there (P=.05, P=.01). We also want to try and learn look at genes significant under FDR=.1 and FDR=.05 (A previous student had done this for a different expression pattern). Unfortunately noone left in my lab knows how to use R and I cant figure out the code :( Can anyone help me??