Dear Bioconductor member,
I am quite a self-learning debutant with microarray analysis, but I managed to perform simple Quality Control, Preprocessing and DE analysis using affy and limma packages
But now, I am starting to work with Gene ST array and I will soon have to work with Raw data from HTA array.
So I tried to convert myself to the oligo package, however, the documentation for this package is directed to the HGU95, and it is not easily adaptable to the Gene ST for a neophyte like me.
So my question for you is : Do you know of more recent information about the use of the oligo package with recent WT microarrays.
I also have a few questions that arise for my first tries with oligo
- On GEO, they had, in my case,
.rma-gene-full.chpfiles. Are the
- After reading the
CELfiles, I got a GeneFeatureSet (called
exprs(data)doesn't have probes names as row names ? Is it normal ? Is it a problem ? How to fix it ?
- Why is it that :
> length(featureNames(data))  2598544 > length(probeNames(data))  1025088 > data.rma = rma(data) > length(featureNames(data.rma))  53617 > data.rma = rma(data, target="probeset") > length(featureNames(data.rma))  352859
- After I perform rma, I get row names for
exprs(data.rma), but those are just numbers from 16650001 to 17127721 (not linear though)
- Oligo found the annotation himself pd.hugene.2.0.st), and attached it to the GeneFeatureSet, but what does that mean ? How to access theses annotations ?
I would be very thankful if you could explain some of these to me ! (or at least provide me relevant documentation)