The information the cdf file is giving me seems misleading: nbrOfCells(cdf) # 4,691,556 cellIndices <- getCellIndices(cdf) #length(unlist(cellIndices)) # 4,358,832
The number of cells does not match the cell indices. ?? On May 18, 7:41 pm, Irene Pylypenko <ipylype...@gmail.com> wrote: > chipType <- "Hs_PromPR_v02" > cdf <- AffymetrixCdfFile$byChipType(chipType, verbose=verbose) > cs <- AffymetrixCelSet$byName("GSE17125", cdf=cdf, verbose=verbose) > acp <- AromaCellPositionFile$byChipType(chipType) > #dim 4359744 2 > data <- extractMatrix(cs) > #dim: 4691556 66 > > On May 17, 5:29 pm, Henrik Bengtsson <henrik.bengts...@aroma- > > project.org> wrote: > > Hi, > > > which chip type and CDF are you thinking of? Even better, please show > > the code how you got those numbers and we take it from there. > > > /Henrik > > > On Tue, May 17, 2011 at 1:53 PM, Irene Pylypenko <ipylype...@gmail.com> > > wrote: > > > Hello, > > > How do I find the genomic location of each probe (cell)? Specifically, > > > a chromosome # and start site. Is this information stored in a > > > AffymetrixCelSet object? > > > I know the cdf object contains this information, via the > > > AromaCellPositionFile file, but this gives me 4,359,744 probes, where > > > as AffymetrixCelSet gives me 4,691,556. So I was wondering how I could > > > map these two files. > > > I know about the UGP files, but I believe it gives the unit locations, > > > whereas I'm interested in probe location. > > > Thanks, > > > Irene > > > > -- > > > When reporting problems on aroma.affymetrix, make sure 1) to run the > > > latest version of the package, 2) to report the output of sessionInfo() > > > and traceback(), and 3) to post a complete code example. > > > > You received this message because you are subscribed to the Google Groups > > > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/. > > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/