Dear All,

I am trying to process an affymetrix miRNA microarray that is shown to have 7815 rownames (miRNA identifiers). When I read the CEL files with ReadAffy() function :

RAW <- ReadAffy()

dim(exprs(RAW)) yields 52900 probes where there should be 7815. Affybatch object also says that there are 7815 genes but why expression file of the Affybatch object shows up 52900 rows ? This is dealt with in rma() normalization and there stays correctly 7815 rows but other normalization packages (vsn, ExiMiR) cannot deal with this and there remains 52900 probes after normalization. I would appreciate if you could let me know what is going on. Thanks 

With kind regards,

Alperen Taciroglu

Affy arrays have multiple 25-mers that together are intended to measure a single transcript. This is silly in the case of the miRNA arrays, as the target is shorter than the oligo that is used to measure (and there are multiple identical 25-mers for each miRNA).

Anyway, that's why there are more probes before you normalize. Also note that the vsn package has a function called vsnrma() that does understand what to do with Affy arrays.

What do you get from

cdfName(RAW)

Affymetrix arrays usually have multiple features (probes) per probe set (targeted gene). Could it be that 7815 is the number of probe sets and 52900 the number of probes?

Wolfgang