Dear aroma team,
I am using aroma.affymetrix for the exon array and I am having trouble using one of your custom .CDF files. It is the one for core transcripts: “ HuEx-1_0-st-v2,coreR3,A20071112,EP.CDF<http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf>”, listed in http://aroma-project.org/node/122, under R3. I get an error when setting up the cel set with that .CDF file: there seems to be a mismatch between the number of cells on the .CDF file and on the .CEL files (please, see below). I report the output of sessionInfo() and traceback() after the code. I have tried several other of your custom .CDF files (R3: extended and full, R2: core) and I do not get any errors. I am actually using one .CDF file called “HuEx-1_0-st-v2,core,A20071112,EP.CDF<http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf>” that works just fine. The only difference in the name is the missing R3 and I only realized after my supervisor tried to test my script. I downloaded it one year ago and I assumed it was yours, but I cannot remember where I got it from and cannot trace it back. I have downloaded the core R3 .CDF file several times from http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf, to make sure I have the right version. Do you think there might be something wrong about the available file? Any ideas on how to solve this problem? Thank you very much for your help. Best, Maria Rodrigo > ds <- "AffyColonCancer" > chipType <- "HuEx-1_0-st-v2" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags = "coreR3,A20071112,EP") > cs <- AffymetrixCelSet$byName(ds, cdf = cdf) Error in method(static, ...) : [2012-08-15 12:47:07] Exception: Failed to setup a data set for any of 1 data directories located. The following reasons were reported: (1) Cannot set CDF. The specified CDF structure ('HuEx-1_0-st-v2,coreR3,A20071112,EP') is not compatible with the chip type ('HuEx-1_0-st-v2') of the CEL file. The number of cells do not match: 33280 != 6553600 (while trying 'rawData/AffyColonCancer/HuEx-1_0-st-v2'). at #02. method(static, ...) - method() is in environment 'aroma.affymetrix' at #01. AffymetrixCelSet$byName(ds, cdf = cdf) - AffymetrixCelSet$byName() is local of the calling function > sessionInfo() R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C [5] LC_TIME=Danish_Denmark.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_2.5.0 affxparser_1.28.1 aroma.apd_0.2.3 R.huge_0.4.1 aroma.core_2.5.0 aroma.light_1.24.0 [7] matrixStats_0.5.2 R.rsp_0.8.2 R.devices_2.1.1 R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2 [13] R.utils_1.12.1 R.oo_1.9.8 R.methodsS3_1.4.2 BiocInstaller_1.4.7 loaded via a namespace (and not attached): [1] tools_2.15.1 > traceback() 11: modStop(cond) 10: abort.condition(cond) 9: abort(cond) 8: abort.default(msg, call = call) 7: abort(msg, call = call) 6: throw.Exception(Exception(...)) 5: throw(Exception(...)) 4: throw.default(msg) 3: throw(msg) 2: method(static, ...) 1: AffymetrixCelSet$byName(ds, cdf = cdf) -- 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/
