2009/8/13 tea <ywcu...@gmail.com>:
>
> Dear all,
>
> I ran aroma.affymetrix using two different custom CDF (one for entrez,
> one fore refseq)
> I was supposed to get different # of probesets.
> For the entrez-based custom CDF, the total # of probesets shoud be
> 11911+(probesets with the name AFFY...)
> For the refseq-based custom CDF, the total # of probesets should be
> 19692+(probesets with the name AFFY...)
> However, I got the total # of probesets in the final RMA-summarized
> expression matrix is 11980
> for both cases, which seemed to me that aroma.affymatrix might have
> some setting for the maximum # of probesets in an calculation. I was
> wondering how to set this parameter so that the expression index of
> all the probesets are reported.
I hope my answer to your Aug 14, 2009 thread 'Question about
difference in total number of probesets between affy(rma) and
aroma.affymetrix' clarify what is going on.
There is no such parameter that sets the maximum number of units
("probesets") processed.
/Henrik
>
> Thank you very much.
>
> Sincerely,
>
> Yiwen Chen
> >
>
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