Hi, I have run into a problem reading .cel files with aroma.affymetrix. I am attempting to read in just a single .cel file - this was originally in binary format (v4), but after downloading the HuEx-1_0-st-v2.cdf file from the affy website, I realized I would need to convert to ASCII (v3). I went ahead and did that, but am still getting a cryptic error. Code follows, with comments interspersed.
> library(aroma.affymetrix) Loading required package: R.utils Loading required package: R.oo Loading required package: R.methodsS3 R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help. R.oo v1.8.1 (2011-07-10) successfully loaded. See ?R.oo for help. R.utils v1.7.8 (2011-07-24) successfully loaded. See ?R.utils for help. Loading required package: R.filesets Loading required package: digest R.filesets v1.1.0 (2011-07-24) successfully loaded. See ?R.filesets for help. Loading required package: aroma.core Loading required package: R.cache R.cache v0.4.3 (2011-07-21) successfully loaded. See ?R.cache for help. Attaching package: 'R.cache' The following object(s) are masked from 'package:R.filesets': getChecksum Loading required package: R.rsp R.rsp v0.6.2 (2011-07-27) successfully loaded. See ?R.rsp for help. Type browseRsp() to open the RSP main menu in your browser. Loading required package: matrixStats matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for help. Loading required package: aroma.light aroma.light v1.20.0 (2011-04-12) successfully loaded. See ?aroma.light for help. aroma.core v2.1.4 (2011-08-02) successfully loaded. See ?aroma.core for help. Attaching package: 'aroma.core' The following object(s) are masked from 'package:base': .Machine, append, apply, cat, colMeans, colSums, getOption, lapply, library, require, sapply Loading required package: aroma.apd Loading required package: R.huge R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for help. Loading required package: affxparser aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help. aroma.affymetrix v2.1.6 (2011-07-27) successfully loaded. See ? aroma.affymetrix for help. There were 13 warnings (use warnings() to see them) Package appears to load fine.... Now I read the .cdf file, which is located in the proper directory: > cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2") > cdf AffymetrixCdfFile: Path: annotationData/chipTypes/HuEx-1_0-st-v2 Filename: HuEx-1_0-st-v2.cdf Filesize: 933.84MB Chip type: HuEx-1_0-st-v2 RAM: 0.00MB File format: v3 (text; ASCII) Dimension: 2560x2560 Number of cells: 6553600 Number of units: 1432154 Cells per unit: 4.58 Number of QC units: 0 All good up to here. The following performs the troubleshooting steps to ensure that the data directory structure is correct (direct from the aroma-affymetrix site): > library("R.utils"); > pathR <- Arguments$getReadablePath("rawData/", mustExist=TRUE); > dataSet <- "prostate"; > pathD <- Arguments$getReadablePath(dataSet, path=pathR, mustExist=TRUE); > chipType <- "HuEx-1_0-st-v2"; > chipTypeS <- gsub(",.*", "", chipType); > pathDC <- Arguments$getReadablePath(chipTypeS, path=pathD, mustExist=TRUE); > print(list.files(path=pathDC)); [1] "GSM526134_YX_Exon1_PCA0001.CEL" Everything appears to be in order. But now, when I try to read the cel file: > csR <- AffymetrixCelSet$byName("prostate", cdf=cdf); Error in list(`AffymetrixCelSet$byName("prostate", cdf = cdf)` = <environment>, : [2011-08-10 14:59:25] 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 direct at throw(sprintf("Failed to setup a data set for any of %d data directories lo at method(static, ...) at AffymetrixCelSet$byName("prostate", cdf = cdf) I'm baffled by this error message... Here are the results of print(sessionInfo()): > print(sessionInfo()) R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.affymetrix_2.1.6 affxparser_1.22.1 aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.1.4 [6] aroma.light_1.20.0 matrixStats_0.2.2 R.rsp_0.6.2 R.cache_0.4.3 R.filesets_1.1.0 [11] digest_0.5.0 R.utils_1.7.8 R.oo_1.8.1 R.methodsS3_1.2.1 Any help would be greatly appreciated. Thanks, Matt -- 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/