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 <aisyah...@gmail.com> 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.
>> >
>> >
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>
> --
> --
> 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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