[BioC] subsetting an eset object with a defined list

[alex lam (RI)]

Hi Celine,

This works for me:
> exprs(eset.norm.loess)[c("1007_s_at","1053_at"),1:3]
          1333_01_rep1.cel 1333_01_rep2.cel 1333_02_rep1.cel
1007_s_at         3.831777         4.275516         4.425432
1053_at           6.940475         7.138406         6.852670

So if your list of genes is a vector, I think you just put

> exprs(eset)[your list,1:19]

If you list is not a vector, as.vector might help.

Thanks,
Alex

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Celine
Carret
Sent: 05 October 2006 11:28
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] subsetting an eset object with a defined list

Hi,
I'm stuck remembering the way of subsetting an eset object (19 affy
arrays) to accomodate only a defined list of genes that I'm interested
in.
I read.table(list) into R, transformed it as.matrix and use the
functions:
exprs(eset)[list] or
exprs(eset)[as.character(list)]

those functions recognize that I have 904 genes in that list, but gives
me 904 NA What I would like to obtain is my 904 genes with the values
for the 19 arrays, in order to assess the DE only on this subgroup as
the other genes are not supposed to be expressed at this stage of the
cultures I'm looking at.
Could someone please point me in the right direction?
Thank you very much
Celine



sessionInfo()
Version 2.3.0 (2006-04-24)
ia64-unknown-linux-gnu

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"
"grDevices"
[7] "utils"     "datasets"  "base"    

other attached packages:
affycoretools       GOstats      Category      hgu95av2          KEGG
      "1.4.0"       "1.6.0"       "1.4.1"      "1.12.0"      "1.12.0"
     multtest    genefilter      survival        xtable          RBGL
     "1.10.2"      "1.10.1"        "2.24"       "1.3-2"       "1.8.1"
     annotate            GO         graph         Ruuid         limma
     "1.10.0"      "1.12.0"      "1.10.6"       "1.9.2"      "2.7.10"
         affy        affyio       Biobase
     "1.10.0"      "0.99.3"      "1.10.1"


--
----------------------------------------------------
Celine Carret PhD
Pathogen Microarrays group
The Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK.
tel. +44 (0)1223 494 940
fax. +44 (0)1223 494 919
email: ckc at sanger.ac.uk
http://www.sanger.ac.uk/PostGenomics/PathogenArrays/

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