Hi. It's all about the concept of "unique CDF" versus the regular CDF, cf.
http://aroma-project.org/vignettes/MAT-TilingArrayAnalysis The following shows how to do it: > chipType <- "Hs_PromPR_v02"; # Default CDF > cdf <- AffymetrixCdfFile$byChipType(chipType); > print(cdf); AffymetrixCdfFile: Path: annotationData/chipTypes/Hs_PromPR_v02 Filename: Hs_PromPR_v02.cdf Filesize: 61.95MB Chip type: Hs_PromPR_v02 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2166x2166 Number of cells: 4691556 Number of units: 23155 Cells per unit: 202.62 Number of QC units: 0 # "Unique" based on the default CDF, that is, use only cells # (probes) that are map uniquely to the genome, cf. # http://aroma-project.org/vignettes/MAT-TilingArrayAnalysis > cdfU <- getUniqueCdf(cdf); > print(getChipType(cdfU)); [1] "Hs_PromPR_v02,unique" # Get the genomic positions per cell for the *unique* CDF. > acp <- AromaCellPositionFile$byChipType(getChipType(cdfU)); > print(acp); AromaCellPositionFile: Name: Hs_PromPR_v02 Tags: unique Full name: Hs_PromPR_v02,unique Pathname: annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02,unique.acp File size: 20.79 MB (21798905 bytes) RAM: 0.00 MB Number of data rows: 4359744 File format: v1 Dimensions: 4359744x2 Column classes: integer, integer Number of bytes per column: 1, 4 Footer: <createdOn>20081209 10:26:40 EST</createdOn><platform>Affymetrix</platform><chipType>Hs_PromPR_v02</chipType> Chip type: Hs_PromPR_v02 Platform: Affymetrix Especially note how getChipType(cdfU) is used instead of getChipType(cdf) when retrieving the ACP file. Hope this helps /Henrik On Fri, May 20, 2011 at 3:35 PM, Irene Pylypenko <ipylype...@gmail.com> wrote: > 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/ > -- 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/
