Hi all I am struggling with the RES file format of affymatrix U133+2 platform and its interpretation of P/M/A calls inferences. My specific queries are :
(1) For calculating expression data for a particular gene in that file, many genes are represented by more than one probe_set ids. So, I averaged probeset ids' values related to each gene. Is it right way to do this?
(2) Do I have to exclude the values of expression corresponding to M and A notation ? Because, my presumption is that only P is significant and should be taken into account for calculating expression data.
(3) These absolute values are fold changes (overexpression) or what ? And are these values compared with those of normal conditions; if this is the case, then what was the control/normal for each cell line? Was it same or different for each cell line? because in my data file I see all the values are above zero (0) only which give the impression that neither of gene was downregulated !! Is it the case.
Or suggest me where I can proper information regarding RES file format and calculation of gene expression from this file format.
Please suggest the needful