Hi. On Mon, Mar 14, 2011 at 10:54 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Myrto, > > On 3/14/2011 7:58 AM, Myrto Kostadima wrote: >> >> Hi, >> I am currently trying to analyse microarray data from this publicly >> available dataset: >> GSE24759<http: www.ncbi.nlm.nih.gov="" geo="" query="" acc.cgi?acc="GSE24759"> >> Platform: [U133AAofAv2] Affymetrix GeneChip HT-HG_U133A Early Access Array >> >> When using gcrma on the data: >>> >>> marray.eset.gcrma<- gcrma(marray.data) >> >> I get the following error: >> >> [1] "Environment u133aaofav2probe was not found in the Bioconductor >> repository." >> Error in get(probepackagename) : object 'u133aaofav2probe' not found >> >> The only package that is available on Bioconducttor is: u133aaofav2cdf >> >> I have not been able to find a solution online. Anybody who could help >> with >> that? > > Unfortunately we have never been able to get hold of the probe file for this > array, so have not been able to make the probe package. If anybody out there > happens to have the probe file, I would appreciate an off-line response. >From http://aroma-project.org/chipTypes/HT_HG-U133A_and_HT_HG-U133B "Early access versions of the HT_HT-U133A chip type were labelled U133AAofAv2(*) and HT_HT-U133A_EA. Footnote: (*) The evidence for this comes from comparing spatial images of a CEL file with U133AAofAv2 [link to PNG] in the header with one with HT_HT-U133A [link to PNG]. Both have the same spatial patterns, i.e. blocks of checkered blocks and control probes, "landing lights", and positive controls spelling out 'Genechip' and 'HG-U133 AofAv2'." For advanced users only: The convertCel() function of affxparser allows you to *relabel* the chip type *label* that exists in the CEL file header, e.g. convertCel("old.CEL", "new.CEL", newChipType="HT_HT-U133A"). Warning: Only do this if you know what you're doing. Read help("convertCel", package="affxparser") in the devel-version affxparser 1.23.3 contains more info. Again, do not use this if you are not fully understanding what you are doing. If misused, you're analysis will be completely garbage. If I wasn't clear enough, read this paragraph again. If you still don't understand it, pretend that you never heard about this new feature of convertCel(), i.e. wipe it out of your memory. I hope I made my point. /Henrik > > > Best, > > Jim > > >> >> Thanks, >> Myrto >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >