On Jan 3, 2015 2:54 AM, "Amon" <aisyah...@gmail.com> wrote:
>
> Hi Henrik,
>
> Thanks for the tip; I did try clearing the cache as you suggested as well
as running it on --vanilla but the same error appeared. In the interests of
saving time, I've rerun the whole process on my personal laptop, which has
an up-to-date version of R (I used an external server previously, so no
admin privileges), and it ran without any problems... so that was probably
the issue.
Good to hear.
It's still weird to me because weekly redundancy test on exactly this is
known to have worked for years without issues. I would blame neither R nor
affxparser but some random hiccup during installation on that particular
machine.
You might f find it useful to know that you can install R from source on
user accounts with very little privileges ... and it's fairly easy if the
compilers are up to date.
Henrik
>
> Many thanks again.
>
> Aisyah
>
> On Saturday, January 3, 2015 7:53:13 AM UTC+8, Henrik Bengtsson wrote:
>>
>> I fail to reproduce this with R 3.0.2 and affxparser 1.34.4 and
>> aroma.affymetrix_2.12.8 and the same data file (just like you).
>>
>> However, from code inspection it could be that you have some cached
>> results from an earlier run that used a CDF with the exact same
>> filename but with an actually different content - could that be the
>> case? (I'll try to close that pitfall in the next release). If this
>> is the problem, then try to clear your cache. The content in
>> ~/.Rcache/ is non-critical and can be deleted at any time. You can
>> erase the cache like this:
>>
>> > library("R.cache")
>> > clearCache()
>> Are you really sure you want to delete the 184 files and 16
>> directories in '/home/JohnDoe/.Rcache'? [y/N]: y
>>
>> The only thing you'll notice is that some steps will be slow when you
>> run the first time after clearing the cache. This is the Aroma
>> Framework recalculating/regenerated part of the cache.
>>
>> Let me know if this works. If not, other ideas are:
>>
>> * You seem to have other packages loaded/attached too. Retry in a
>> fresh R session, e.g. R --vanilla.
>>
>> * Your R version and therefore your affxparser versions are outdated.
>> I would retry with a recent version of R, i.e. R >= 3.1.2.
>>
>> /Henrik
>>
>>
>> On Mon, Dec 29, 2014 at 5:20 PM, Amon <aisy...@gmail.com> wrote:
>> > Below is the output (for the binary, not text, CEL file) :
>> >
>> >> cf <- cs[[1]]
>> >> print(cf) # Should be the 'EA_BT549' CEL file
>> > AffymetrixCelFile:
>> > 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> 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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>> >> >> >
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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()
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>> >> > traceback(), and 3) to post a complete code example.
>> >> >
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>> > --
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>> > version of the package, 2) to report the output of sessionInfo() and
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>> >
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> --
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