Below is the output (for the binary, not text, CEL file) : > cf <- cs[[1]]> print(cf) # Should be the 'EA_BT549' CEL > fileAffymetrixCelFile: Name: EA_BT549 Tags: Full name: EA_BT549 Pathname: rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL File size: 63.16 MB (66226783 bytes) RAM: 0.01 MB File format: v4 (binary; XDA) Platform: Affymetrix Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP Timestamp: 2007-08-30 20:27:52> str(getHeader(cf))List of 14 $ filename : chr "rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL" $ version : int 4 $ cols : int 2560 $ rows : int 2560 $ total : int 6553600 $ algorithm : chr "Percentile" $ parameters : chr "Percentile:75;CellMargin:4;OutlierHigh:1.500;OutlierLow:1.004;AlgVersion:6.0;FixedCellSize:TRUE;FullFeatureWidth:7;FullFeatureH"| __truncated__ $ chiptype : chr "HuEx-1_0-st-v2" $ header : chr "Cols=2560\nRows=2560\nTotalX=2560\nTotalY=2560\nOffsetX=0\nOffsetY=0\nGridCornerUL=617 453\nGridCornerUR=18881 579\nGridCornerL"| __truncated__ $ datheader : chr "[0..65534] 0293_BT549:CLS=19341RWS=19341XIN=0 YIN=0 VE=30 2.0 08/30/07 20:27:52 54716690 M10 \024 \024 HuEx-1_0-s"| __truncated__ $ librarypackage: chr "" $ cellmargin : int 4 $ noutliers : int 172409 $ nmasked : int 0
If it helps for you to visually inspect the file yourself, I downloaded this file from a publicly available dataset here http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-181/samples/ BT549 is the 8th row from the top I think. Best Aisyah On Tuesday, December 30, 2014 9:11:26 AM UTC+8, Henrik Bengtsson wrote: > > It turns out this error is triggered inside affxparser::updateCel() > and it looks like it can happen for two reasons, where one is due to a > corrupt/corruptly read CEL header. What does > > > cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2", > tags="fullR3,A20071112,EP") > > cs <- AffymetrixCelSet$byName("myData", cdf=cdf) > > cf <- cs[[1]] > > print(cf) # Should be the 'EA_BT549' CEL file > > str(getHeader(cf)) > > output? > > /Henrik > > > On Mon, Dec 29, 2014 at 4:39 PM, Amon <aisy...@gmail.com <javascript:>> > wrote: > > Hi Henrik, thanks for your very prompt response. Below is the error > message > > I got when I tried to run the same code on the unconverted (i.e., > original) > > v4 CEL file. I've reddened the area that alerted me to the possibility > that > > it's the format of the file that caused it not to work (the binary > format > > possibly causes NA values, creating the "missing value where TRUE/FALSE > > needed" error), because as I said I've run this preprocessing step on my > v3 > > data, using the same CDF, many times with no problems before: > > > > 20141229 05:17:51|Background correcting data set... > > 20141229 05:17:51| Number of arrays: 1 > > 20141229 05:17:51| Array #1 ('EA_BT549') of 1... > > 20141229 05:17:52| Adjusting PM signals only > > 20141229 05:17:52| Obtaining signals... > > 20141229 05:17:53| Obtaining signals...done > > 20141229 05:17:53| Applying normal+exponential signal model... > > 20141229 05:17:55| Applying normal+exponential signal model...done > > 20141229 05:17:55| Writing adjusted probe signals... > > 20141229 05:17:55| Adding temporary suffix from file... > > 20141229 05:17:55| Pathname: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL > > 20141229 05:17:55| Suffix: .tmp > > 20141229 05:17:55| Rename existing file?: FALSE > > 20141229 05:17:55| Temporary pathname: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp > > 20141229 05:17:55| Adding temporary suffix from file...done > > 20141229 05:17:55| Creating CEL file for results, if missing... > > 20141229 05:17:55| Creating CEL file... > > 20141229 05:17:55| Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP > > 20141229 05:17:55| Pathname: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp > > 20141229 05:17:55| Adding temporary suffix from file... > > 20141229 05:17:55| Pathname: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp > > 20141229 05:17:55| Suffix: .tmp > > 20141229 05:17:55| Rename existing file?: FALSE > > 20141229 05:17:55| Temporary pathname: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp > > 20141229 05:17:55| Adding temporary suffix from file...done > > 20141229 05:17:55| Method 'copy'... > > 20141229 05:17:55| Copying file safely... > > 20141229 05:17:55| Source: > rawData/myData/HuEx-1_0-st-v2/EA_BT549.CEL > > 20141229 05:17:55| Destination: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp > > 20141229 05:17:55| Copying to temporary file using file.copy()... > > 20141229 05:17:57| Copying to temporary file using > file.copy()...done > > 20141229 05:17:57| Renaming temporary file to destination name... > > 20141229 05:17:57| Renaming temporary file to destination > name...done > > 20141229 05:17:57| Validating destination file... > > 20141229 05:17:57| Validating destination file...done > > 20141229 05:17:57| Copying file safely...done > > 20141229 05:17:57| Renaming AffymetrixCelFile pathname... > > 20141229 05:17:57| Source: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp > > 20141229 05:17:57| Destination: > > probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp > > 20141229 05:17:57| Renaming file... > > 20141229 05:17:57| Renaming file...done > > 20141229 05:17:57| Renaming AffymetrixCelFile pathname...done > > 20141229 05:17:57| Method 'copy'...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: 63.16 MB (66226783 bytes) > > RAM: 0.00 MB > > File format: v4 (binary; XDA) > > Platform: Affymetrix > > Chip type: HuEx-1_0-st-v2,fullR3,A20071112,EP > > Timestamp: 2007-08-30 20:27:52 > > 20141229 05:17:58| Creating CEL file...done > > 20141229 05:17:58| Creating CEL file for results, if missing...done > > 20141229 05:17:58| Writing adjusted intensities... > > Error in if (r[1] < 1 || r[2] > nbrOfCells) { : > > missing value where TRUE/FALSE needed > > 20141229 05:17:59| Writing adjusted intensities...done > > 20141229 05:17:59| Writing adjusted probe signals...done > > 20141229 05:17:59| Array #1 ('EA_BT549') of 1...done > > 20141229 05:17:59|Background correcting data set...done > > > > > > As a result, no csBC object is created. > > > > Aisyah > > > > > > On Tuesday, December 30, 2014 6:55:59 AM UTC+8, Henrik Bengtsson wrote: > >> > >> On Mon, Dec 29, 2014 at 1:37 PM, Amon <aisy...@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-af...@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-affymetr...@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-af...@googlegroups.com > <javascript:> > > 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-affymetr...@googlegroups.com <javascript:>. > > 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.
