[BioC] pm values
Stephen Henderson
s.henderson at ucl.ac.uk
Mon Apr 14 16:18:58 MEST 2003
Sorry I have been looking through the vignette on Affy but am still a bit
confused hot to extract the probe level data I need.
I have an AffyBatch object with ca 43 (U133A) samples. Ihave 5 genes of
interest that I wish to examine the probes.
>Bigbatch
> genes
[1] "blahbla_s_at" "blahbla_s_at" "blahbla_s_at" "blahbla_s_at"
[5] "blahbla_s_at"
I then try
>place<- pmindex(bigbatch, genes)
or even
>place<- pmindex(bigbatch, genes, xy=TRUE)
This gives me a list of 5 sets of vectors, or 5 sets of coordinates.
Now when I try
>pm(bigbatch)[place[[1]]]
or all sorts of variants e.g.
pm(bigbatch)[,place[[1]]]
I don't get the probes I am looking for at all "blahbla_s_at1 "blahbla_s_at2
etc. What do I need to be doing?
Thanks
Stephen
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