[BioC] .EXP files

[Sean Davis]

On 3/10/06 6:48 PM, "LUIS F MENEZES" <lmenezes at jhmi.edu> wrote:

> Hi,
> I am trying to work with GEO dataset GSE2180, containing time-series
> experiments including 10 time points for 4
> different genotypes. The files include the .CEL and .EXP, these last ones
> containing the experimental information
> (genotype and time point). How can I combine the .CEL and .EXP? Thank you.

Luis,

Since there is a GEO dataset, GDS1319, that represents GSE2180, this is
quite easy to do with the GEOquery package.  To make an exprSet, you just
need a couple of commands.  The experiment information is automatically
parsed out and placed in the pData slot of the exprSet.

Hope this helps.

Sean


> library(GEOquery)
> gds <- getGEO('GDS1319')
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/data/gds/soft_gz/GDS1319.soft.gz'
ftp data connection made, file length 9181833 bytes
opened URL
==================================================
downloaded 8966Kb

File stored at: 
/tmp/Rtmp2jTUmw/GDS1319.soft.gz
parsing geodata
parsing subsets
ready to return
> eset <- GDS2eSet(gds)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material.
    To view, simply type 'openVignette()' or start with 'help(Biobase)'.
    For details on reading vignettes, see the openVignette help page.

> eset
Expression Set (exprSet) with
    22625 genes
    123 samples
         phenoData object with 4 variables and 123 cases
     varLabels
        : sample
        : genotype/variation
        : time
        : description