gcrma - u133aaofav2probe error
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@myrto-kostadima-4542
Last seen 7.3 years ago
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? Thanks, Myrto -- Myrto Areti Kostadima PhD Student - Paul Bertone Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK [[alternative HTML version deleted]]
Microarray gcrma marray Microarray gcrma marray • 923 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
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. 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
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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 >
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