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.

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

LUIS F MENEZES 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. Do you need to do this? Is the information already exposed in the GSE files (GEO Soft format) which you can easily access using Sean Davis' GEOquery: http://www.bioconductor.org/packages/bioc/1.8/html/GEOquery.html http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE2180 Peter