[BioC] probe level data with aroma.affymetrix

Henrik Bengtsson hb at stat.berkeley.edu
Fri Jan 25 06:55:34 CET 2008


Hi,

since aroma.affymetrix is not on BioC, please post your questions to
the aroma.affymetrix mailing list instead.  I will answer your
question there in due time.

/Henrik


On Jan 24, 2008 9:47 PM, Yuan Jian <jayuan2008 at yahoo.com> wrote:
> Hello,
>   in affy package, we can get probe level raw data using pm or mm methods as below:
>
>   > library("affydata")
>   > data(Dilution)
>   > pm(Dilution, "1001_at")[1:3, ]
>
>                  20A  20B  10A 10B
>   1001_at1 129 93 130 73.8
>   ...
>
>   if I use aroma.affymetrix as below:
>   > cs <- AffymetrixCelSet$fromName("anth", chipType="HuEx-1_0-st-v2")
> > cdf <- AffymetrixCdfFile$fromChipType("HuEx-1_0-st-v2");
> > setCdf(ds, cdf);
>
>   how can I get pm or mm data from cs. something like >pm(cs, "1001_at")[1:3,]?
>
>
>   thanks
>   yuan
>
>
>
>
> ---------------------------------
>
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