[aroma.affymetrix] more than two groups analysis using FIRMA

I have the same question with this one. Hope for help. Thanks, Chunjiang -- two group comparison using FIRMA score for exon 1.0 ST array Options SBA View profile More options Nov 2, 12:12 pm Hi Mark, Elizabeth and Aroma team, I have successfully run aroma on my 15

Re: [aroma.affymetrix] Re: exon array analysis errors

Hi Yu Chuan. I'm still mystified by this. Can you check that the PLM was successfully fit? Pull out some chip effects, maybe. Cheers, Mark On 25-Nov-09, at 4:51 AM, Yu Chuan wrote: > Mark, > > I think the below info. may help too. Looks like all the gene-level > NUSE are 0. How could this h

Re: [aroma.affymetrix] Re: apt- affymetrix power tool

Hi Elai/Zaid. You'll want to be careful with all this (i.e. linear models on unnormalized data ... or maybe you are standardizing some other way), but yes you can run the probe level model fits on any AffymetrixCelSet object. The standard RMA procedure would BG adjust, then quantile normali