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.
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 * Your R version and therefore your affxparser versions are outdated.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 <javascript:>>
> 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.
> >> >> >
> >> >> >
> >> >> > 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
> >> > To unsubscribe and other options, go to
> >> > http://www.aroma-project.org/forum/
> >> >
> >> > ---
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> >> > To unsubscribe from this group and stop receiving emails from it,
> send
> >> > an
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> >> > 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.
> >
> >
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> <javascript:>
> > To unsubscribe and other options, go to
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> >
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--
--
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