I've come across an ambiguity concerning reading and analysing two-channel Agilent microarray data.
The function I use to read the data in is read.maimages with the defaults (gMedianSignal, rMedianSignal, gMedianSignal, rMedianSignal) except for annotation columns.
As a result of the analysis I obtained a list of genes, but in some cases I observe the following problem: when I look in the raw data files (for some genes) there is LogRatio = 0 and corresponding p-value equal to 1 whereas the same genes are listed as significantly differentially expressed - after my analysis using limma.
I really have no idea where the ploblem lies - I assume that Feature Extraction Software provided by Agilent uses different columns for calcutation of LogRatio - should I read the data in in a different way (e.g. using gProcessedSignal etc.)?
I would really appreciate your help,