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: 120141229 05:17:51| Array #1 ('EA_BT549') of 1...20141229 05:17:52|
Adjusting PM signals only20141229 05:17:52| Obtaining signals...20141229
05:17:53| Obtaining signals...done20141229 05:17:53| Applying
normal+exponential signal model...20141229 05:17:55| Applying
normal+exponential signal model...done20141229 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.CEL20141229 05:17:55| Suffix:
.tmp20141229 05:17:55| Rename existing file?: FALSE20141229 05:17:55|
Temporary pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp20141229 05:17:55| Adding
temporary suffix from file...done20141229 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,EP20141229 05:17:55|
Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp20141229
05:17:55| Adding temporary suffix from file...20141229 05:17:55|
Pathname: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp20141229
05:17:55| Suffix: .tmp20141229 05:17:55| Rename existing file?:
FALSE20141229 05:17:55| Temporary pathname:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp20141229 05:17:55|
Adding temporary suffix from file...done20141229 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.CEL20141229 05:17:55|
Destination: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp20141229
05:17:55| Copying to temporary file using file.copy()...20141229
05:17:57| Copying to temporary file using file.copy()...done20141229
05:17:57| Renaming temporary file to destination name...20141229
05:17:57| Renaming temporary file to destination name...done20141229
05:17:57| Validating destination file...20141229 05:17:57|
Validating destination file...done20141229 05:17:57| Copying file
safely...done20141229 05:17:57| Renaming AffymetrixCelFile
pathname...20141229 05:17:57| Source:
probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp.tmp20141229 05:17:57|
Destination: probeData/myData,RBC/HuEx-1_0-st-v2/EA_BT549.CEL.tmp20141229
05:17:57| Renaming file...20141229 05:17:57| Renaming
file...done20141229 05:17:57| Renaming AffymetrixCelFile
pathname...done20141229 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 20:27:5220141229 05:17:58| Creating CEL
file...done20141229 05:17:58| Creating CEL file for results, if
missing...done20141229 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...done20141229 05:17:59| Writing adjusted probe
signals...done20141229 05:17:59| Array #1 ('EA_BT549') of 1...done20141229
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 <javascript:>>
> 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.
> >
> >
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