Hi Everyone!

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??  

Hello,

I am using R, bioconductor. I am confused about the user's guide. That's why I am here.I  have gotten as far as sum(GValues<.05) etc. Are those the accurate values? Afterwards based on the previous students notebook they did FDRGValue<-p.adjust(GValues, method="BH") However how they ditermined the number of genes sigfnciant using FDR is confusing. Wouldn't it just be sum(FDRGValues< .05)???? I know I sound like a idiot, that is because when it comes to R I am. I will take a course in it next year but for now I just need help with this so we can identify if we are on the right track with a hypothesis.

I'm really sorry. I'll talk to the previous grad student or a biostats person in my department. Obviously this is bigger than I ever imagined.