Hi Ying. On Fri, Jul 8, 2011 at 10:51 AM, sean nj <njs...@gmail.com> wrote: > I do not know why, but after I converted the custom CDF into binary > CDF and used the binary CDF to do analysis, the analysis went smoothly > without any error message.
Yes, that is/was the cause of your problem. Converting text-based CDFs to binary is the correct way to do it. In earlier version of aroma.affymetrix you would actually have gotten an informative error message explaining this, but thanks to your post I realize that due the recent changes made to how CEL sets are located and loaded, that type of error message does no longer reach the end user and instead you got that less informative error message. I'll see what I can do to preserve that original information. DETAILS: The aroma.affymetrix framework does not allow CDF files in text/ASCII format (very old format) and instead want the CDF in a binary file format. This has do with the fact that text-based CDFs are extremely slow when read. You can read about in Section 'Avoid using ASCII CDFs' on how-to page 'How to: Improve processing time': http://aroma-project.org/howtos/ImproveProcessingTime There is an option [http://www.aroma-project.org/settings] to allow test-based CDFs in aroma, but you don't wanna do that. I'll answer your other questions in a message with an updated topic name. [snip] > Thanks a lot for the help! > > > Ying > > > > > On Jul 8, 10:33 am, sean nj <njs...@gmail.com> wrote: >> Hi guys, >> >> I am new to the aroma.affymetrix package. Here I try to do RMA on >> affy HG-U133_Plus_2 chip CEL files. I can proceed without problem by >> using Henrik's HG-U133_Plus_2,Binary,HB.cdf. But when I tried to use >> BrainArray's custom CDF(Hs133P_Hs_REFSEQ.CDF from the aroma- >> project.org website) as the CDF for my analysis, I got the error >> message. So I >> downloaded the newest version HG-U133_Plus_2,Hs_ENTREZG.cdf from >> BrainArray website and aroma.affymetrix took it as a CDF correctly. >> But when I tried to do >> >> > cs <- AffymetrixCelSet$byName("My_Met_Melanoma", cdf=cdf) >> >> I got the error message again: >> >> Error in list(`AffymetrixCelSet$byName("My_Met_Melanoma", cdf = >> cdf)` = <environment>, : >> Exception: Failed to setup a data set for any of 1 data >> directories located...... >> >> I tried doRMA() and got the same error. >> >> What did I do wrong? Any suggestion? >> [snip] >> >> Thanks a lot for the help! >> >> Ying >> >> > chipType <- "HG-U133_Plus_2" >> > cdf <- AffymetrixCdfFile$byChipType("Hs133P_Hs_REFSEQ") >> >> Error in list(`AffymetrixCdfFile$byChipType("Hs133P_Hs_REFSEQ")` = >> <environment>, : >> >> [2011-07-08 09:45:36] Exception: Could not locate a file for this chip >> type: Hs133P_Hs_REFSEQ >> at throw(Exception(...)) >> at throw.default("Could not locate a file for this chip type: ", >> paste(c(chipTyp >> at throw("Could not locate a file for this chip type: ", >> paste(c(chipType, tags) >> at method(static, ...) >> at AffymetrixCdfFile$byChipType("Hs133P_Hs_REFSEQ")> cdf <- >> AffymetrixCdfFile$byChipType("HG-U133_Plus_2,Hs_ENTREZG") >> > cdf >> >> AffymetrixCdfFile: >> Path: annotationData/chipTypes/HG-U133_Plus_2 >> Filename: HG-U133_Plus_2,Hs_ENTREZG.cdf >> Filesize: 45.03MB >> Chip type: HG-U133_Plus_2,Hs_ENTREZG >> RAM: 0.00MB >> File format: v3 (text; ASCII) >> Dimension: 1164x1164 >> Number of cells: 1354896 >> Number of units: 19070 >> Cells per unit: 71.05 >> Number of QC units: 9> cs <- AffymetrixCelSet$byName("My_Met_Melanoma", >> cdf=cdf) >> >> Error in list(`AffymetrixCelSet$byName("My_Met_Melanoma", cdf = cdf)` >> = <environment>, : >> >> [2011-07-08 09:49:19] Exception: Failed to setup a data set for any of >> 1 data directories located. >> at throw(Exception(...)) >> at throw.default(sprintf("Failed to setup a data set for any of %d >> data director >> at throw(sprintf("Failed to setup a data set for any of %d data >> directories loca >> at method(static, ...) >> at AffymetrixCelSet$byName("My_Met_Melanoma", cdf = cdf)> cdf <- >> AffymetrixCdfFile$byChipType("HG-U133_Plus_2",tags="Binary,HB") >> > cs <- AffymetrixCelSet$byName("My_Met_Melanoma", cdf=cdf) >> > ds <- doRMA("My_Met_Melanoma", chipType="HG-U133_Plus_2,Hs_ENTREZG") >> >> Error in list(`doRMA("My_Met_Melanoma", chipType = "HG- >> U133_Plus_2,Hs_ENTREZG")` = <environment>, : >> >> [2011-07-08 10:05:57] Exception: Failed to setup a data set for any of >> 1 data directories located. >> at throw(Exception(...)) >> at throw.default(sprintf("Failed to setup a data set for any of %d >> data directories located.", lengt >> at throw(sprintf("Failed to setup a data set for any of %d data >> directories located.", length(paths) >> at method(static, ...) >> at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose, >> 50), .onUnknownArgs = "ignore") >> at doRMA.character("My_Met_Melanoma", chipType = "HG- >> U133_Plus_2,Hs_ENTREZG") >> at doRMA("My_Met_Melanoma", chipType = "HG-U133_Plus_2,Hs_ENTREZG") >> >> > sessionInfo() >> >> R version 2.13.0 (2011-04-13) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> [3] LC_MONETARY=English_United States.1252 >> LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] aroma.affymetrix_2.1.0 aroma.apd_0.1.8 >> affxparser_1.24.0 R.huge_0.2.2 >> [5] aroma.core_2.1.0 aroma.light_1.20.0 >> matrixStats_0.2.2 R.rsp_0.5.4 >> [9] R.cache_0.4.2 R.filesets_1.0.2 >> digest_0.5.0 R.utils_1.7.5 >> [13] R.oo_1.8.0 R.methodsS3_1.2.1 >> >> loaded via a namespace (and not attached): >> [1] tools_2.13.0 >> >> >> >> - Hide quoted text - >> >> - Show quoted text - > > -- > 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. 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