On Mon, Dec 29, 2014 at 1:37 PM, Amon <aisyah...@gmail.com> wrote: > Hello, > > I'd like to perform background correction on a HuEx-1_0-st-v2 CEL file that > I've previously converted from xda binary format (Affymetrix v4) to ASCII > text format (Affymetrix v3). I did the file format conversion because aroma > does not work xda-format CEL files,
This is not correct. Where did you read this (because if it's written somewhere it should be corrected)? The aroma.affymetrix package works with the binary/XDA CEL file format too. From the front page of http://aroma-project.org/: "File formats: Works directly with CEL and CDF files (all versions; text/ASCII, binary/XDA, binary/Calvin)." It's unnecessary to convert back to ASCII and it would also slow things down. I would retry with the binary/XDA CEL files and see if you still get the error. If so, I'll look into it. If the error only occurs with ASCII CEL files, I'll add it to the to do list to troubleshoot. Hope this helps Henrik > and I used apt-cel-convert provided by > Affymetrix Power Tools for this conversion. There are several error messages > that come up when I use RmaBackgroundCorrection() on the file, some of which > are: > > 20141229 20:59:04| Cannot create CEL file of version 4 > (probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp). Template CEL file is > of version 3: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL > 20141229 21:00:50| Method 'create'...done > AffymetrixCelFile: > Name: EA_BT549.CEL.tmp > Tags: > Full name: EA_BT549.CEL.tmp > Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp > File size: 62.50 MB (65536700 bytes) > RAM: 0.00 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP > Timestamp: 2014-12-29 20:59:04 > 20141229 21:00:51| Creating CEL file...done > 20141229 21:00:51| Creating CEL file for results, if missing...done > 20141229 21:00:51| Writing adjusted intensities... > Error in if (r[1] < 1 || r[2] > nbrOfCells) { : > missing value where TRUE/FALSE needed > 20141229 21:00:51| Writing adjusted intensities...done > 20141229 21:00:51| Writing adjusted probe signals...done > 20141229 21:00:51| Array #1 ('EA_BT549') of 1...done > 20141229 21:00:51|Background correcting data set...done > > I've provided the full report of the process in the attachment. From the > error message, it seems that the information from the original v4 file has > been retained somehow. Is there an option I can use in the > RmaBackgroundCorrection() function to fix this? Steps I used prior to this > were those found in the aroma page (additionally, I've used this on my v3 > data many times before with no problems): > > chipType <- "HuEx-1_0-st-v2" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags = "fullR3,A20071112,EP") > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > cs <- AffymetrixCelSet$byName("myData", cdf=cdf) > bc <- RmaBackgroundCorrection(cs) > csBC <- process(bc, verbose = verbose) > > ----------------------------------------------------- > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] splines grid parallel stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] Hmisc_3.14-6 Formula_1.1-2 survival_2.37-7 > lattice_0.20-29 aroma.light_2.0.0 > [6] matrixStats_0.10.0 aroma.affymetrix_2.12.8 aroma.core_2.12.8 > R.devices_2.12.0 R.filesets_2.6.0 > [11] affy_1.40.0 Biobase_2.22.0 BiocGenerics_0.8.0 > affxparser_1.34.2 R.utils_1.34.0 > [16] R.oo_1.18.2 R.methodsS3_1.6.2 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.12.1 DNAcopy_1.36.0 PSCBS_0.43.0 > R.cache_0.11.0 R.huge_0.8.0 R.rsp_0.19.6 > [7] RColorBrewer_1.1-2 acepack_1.3-3.3 affyio_1.30.0 > aroma.apd_0.5.0 base64enc_0.1-2 cluster_1.15.3 > [13] digest_0.6.7 foreign_0.8-61 latticeExtra_0.6-26 > nnet_7.3-8 preprocessCore_1.24.0 rpart_4.1-8 > [19] tools_3.0.2 zlibbioc_1.8.0 > > > > Many thanks in advance. > > Aish > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
