Henrick, Thank you for your fast and very clear response! Apologies- the wording of my original post may have been unclear; the .cdf file I obtained from affy was originally in ASCII format, and the cel file was in binary. I assumed (using my own poor intuition, apparently) that the cel file would need to be converted to text as well, as I reasoned that the cdf file would 'expect' a file in the same format (again, error was on my part; not from a specific source). In any case, I have since converted the .cdf to binary using the convertCdf() function in the affxparser package, and rerunning with binary versions of both the cdf and cel file appears to work fine. Thanks again for your assistance - it is much appreciated!
Matt On Aug 11, 11:28 am, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi. > > On Wed, Aug 10, 2011 at 9:13 PM, Matthew Weiser > > <matthew.c.wei...@gmail.com> wrote: > > 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). > > Actually, the aroma framework does not "like" CDF files in ASCII (v3) > format, cf. Section 'rules/allowAsciiCdfs' on the 'Settings' page > [http://aroma-project.org/settings] for an explanation. In other > words, if you keep it in the orginal binary (v4) file format, my guess > is that it will work. > > Please let me know where (e.g. webpage, vignette, ...) you got that > you needed to convert to ASCII- if there is any mistake out there, I'd > like to correct it. > > > > > > > > > > > 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$byChipType("HuEx-1_0-st-v2") > >> cdf > > AffymetrixCdfFile: > > Path: annotationData/chipTypes/HuEx-1_0-st-v2 > > Filename: HuEx-1_0-st-v2.cdf > > Filesize: 933.84MB > > Chip type: HuEx-1_0-st-v2 > > RAM: 0.00MB > > File format: v3 (text; ASCII) > > Dimension: 2560x2560 > > Number of cells: 6553600 > > Number of units: 1432154 > > Cells per unit: 4.58 > > Number of QC units: 0 > > Comment: It is alright to setup/load a CDF in any file format (incl > ASCII (v2)) like this. It is only when it is attached to a CEL > file/set the aroma framework is going to complain (this is the > intended design). > > > > > > > > > > > > > All good up to here. The following performs the troubleshooting steps > > to ensure that the data directory structure is correct (direct from > > the aroma-affymetrix site): > > >> library("R.utils"); > >> pathR <- Arguments$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" > > Yes, your understanding/troubleshooting is completely correct. > > > > > > > > > > > > > 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) > > So, if you just drop you ASCII (v3) CDF file and use the binary (v4) > one instead, it should work like a charm. > > Details/about the error message: A few versions ago, the error message > was actually very informative and explicit about the fact that it > cannot/refuses to setup the data set because the CDF file is in an > ASCII file format. Recently, we added support to setup data sets from > various locations (cf. "...for any of 1 data directories located."). > When an error occur, it moves on and tries with the directory. If none > work, it gives the above generic error message. It's on the todo list > that it should record all error messages generated and report them as > well, which would be useful in your case. > > Hope this helps > > Henrik > > > > > > > > > > > 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 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/
