Yes, it works! I suppose I ought to have checked to make sure I had
the latest version of aroma.affy.
I have to say that the support you provide for your package is
outstanding and I'm very grateful.
Thank you very much!
David
On Aug 31, 1:02 pm, Henrik Bengtsson <henrik.bengts...@bhgc.org>
wrote:
> Hi,
>
> no need for sending me the CEL file - I think I've nailed it. You
> should be able to reproduce the error (iff you have aroma.core
> v2.1.2-v2.1.4 installed) as follows:
>
> library("aroma.affymetrix");
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> acs <- getAromaCellSequenceFile(cdf);
> cells <- getAlleleCellPairs(cdf, verbose=-10);
> pos <- getSnpPositions(acs, cells=cells, verbose=-10);
> # Sanity check
> stopifnot(length(pos) == ncol(cells));
> ## => Error: length(pos) == ncol(cells) is not TRUE
>
> I've fixed this in aroma.core v2.1.5, which you can install by running:
>
> source("http://www.braju.com/R/hbLite.R";);
> hbInstall("aroma.affymetrix");
>
> DETAILS: This "bug" (issue) only affects people using aroma.core
> v2.1.2-v2.1.4 (and that haven't done the same analysis before with
> aroma.core v2.1.1 or before, which in case memoized/cached results
> would have saved you). Regardless of version installed, this was
> just an issue with internal sanity checks, that is, it would not
> affect any of your results.
>
> Hope this solves your problems and thanks to you and Irina Ostrovnaya
> for reporting on this.
>
> /Henrik
>
>
>
>
>
>
>
> On Tue, Aug 30, 2011 at 6:53 PM, DGoode <dgoode.stanf...@gmail.com> wrote:
> > OK, will try to get that .CEL to you.
>
> > I should add that I've reproduced this error with multiple .CEL files.
> > The COTES file was downloaded from TCGA and analysed by a colleague
> > with aroma.affy without any problems.
>
> > Output of df is below:
>
> >> df <- getFile(csR, 1);
> >> print(df);
> > AffymetrixCelFile:
> > Name: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042
> > Tags:
> > Full name: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042
> > Pathname: rawData/Test,set,Data/GenomeWideSNP_6/
> > COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL
> > File size: 65.85 MB (69053496 bytes)
> > RAM: 0.01 MB
> > File format: v4 (binary; XDA)
> > Platform: Affymetrix
> > Chip type: GenomeWideSNP_6,Full
> > Timestamp: 2008-07-13 15:02:08
>
> > On Aug 31, 11:16 am, Henrik Bengtsson <henrik.bengts...@aroma-
> > project.org> wrote:
> >> Hi.
>
> >> On Tue, Aug 30, 2011 at 5:45 PM, DGoode <dgoode.stanf...@gmail.com> wrote:
> >> > Hi Henrik,
>
> >> > I think I got the same output you did - but I've pasted it below for
> >> > you to check if you'd like.
>
> >> > Running diff only turned up differences in spacing at the end of
> >> > lines.
>
> >> Ok.
>
> >> > I'm running Lion (OS X 10.7.1). Could that be contributing to the
> >> > problem?
>
> >> I don't think so.
>
> >> Could you make your
> >> 'COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL' file
> >> available to me so I can try to reproduce it myself? Please gzip it.
>
> >> BTW, if you do
>
> >> df <- getFile(csR, 1);
> >> print(df);
>
> >> what do you get? It should show the above CEL file - if not use
> >> another index for getFile().
>
> >> /Henrik
>
> >> > Thanks,
> >> > David
>
> >> > ##########################################
>
> >> >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> >> >> cdf
>
> >> > AffymetrixCdfFile:
> >> > Path: annotationData/chipTypes/GenomeWideSNP_6
> >> > Filename: GenomeWideSNP_6,Full.CDF
> >> > Filesize: 470.44MB
> >> > Chip type: GenomeWideSNP_6,Full
> >> > RAM: 0.00MB
> >> > File format: v4 (binary; XDA)
> >> > Dimension: 2572x2680
> >> > Number of cells: 6892960
> >> > Number of units: 1881415
> >> > Cells per unit: 3.66
> >> > Number of QC units: 4
> >> >> getChecksum(cdf)
>
> >> > [1] "3fbe0f6e7c8a346105238a3f3d10d4ec"
> >> >> acs <- getAromaCellSequenceFile(cdf);
> >> >> acs
>
> >> > AromaCellSequenceFile:
> >> > Name: GenomeWideSNP_6
> >> > Tags: HB20080710
> >> > Full name: GenomeWideSNP_6,HB20080710
> >> > Pathname: annotationData/chipTypes/GenomeWideSNP_6/
> >> > GenomeWideSNP_6,HB20080710.acs
> >> > File size: 170.92 MB (179217531 bytes)
> >> > RAM: 0.00 MB
> >> > Number of data rows: 6892960
> >> > File format: v1
> >> > Dimensions: 6892960x26
> >> > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> >> > raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> >> > raw
> >> > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> >> > 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> >> > Footer: <createdOn>20080710 22:47:02
> >> > PDT</createdOn><platform>Affymetrix</
> >> > platform><chipType>GenomeWideSNP_6</
> >> > chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</
> >> > filename><filesize>341479928</filesize>
> >> > <checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></
> >> > srcFile><srcFile2>
> >> > <filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</
> >> > filesize>
> >> > <checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2>
> >> > Chip type: GenomeWideSNP_6
> >> > Platform: Affymetrix
> >> >> getChecksum(acs)
>
> >> > [1] "f04f081e0a1900653d957a8f320744c0"
>
> >> > ##########################################
>
> >> > On Aug 31, 4:49 am, Henrik Bengtsson <henrik.bengts...@aroma-
> >> > project.org> wrote:
> >> >> Ok,
>
> >> >> your sessionInfo() looks good. Let's confirm that your annotation
> >> >> data files are correct. Do you get the same as I below - if not, let
> >> >> me know what you get:
>
> >> >> > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> >> >> > cdf
>
> >> >> AffymetrixCdfFile:
> >> >> Path: annotationData/chipTypes/GenomeWideSNP_6
> >> >> Filename: GenomeWideSNP_6,Full.CDF
> >> >> Filesize: 470.44MB
> >> >> Chip type: GenomeWideSNP_6,Full
> >> >> RAM: 0.00MB
> >> >> File format: v4 (binary; XDA)
> >> >> Dimension: 2572x2680
> >> >> Number of cells: 6892960
> >> >> Number of units: 1881415
> >> >> Cells per unit: 3.66
> >> >> Number of QC units: 4> getChecksum(cdf)
>
> >> >> [1] "3fbe0f6e7c8a346105238a3f3d10d4ec"
>
> >> >> > acs <- getAromaCellSequenceFile(cdf);
> >> >> > acs
>
> >> >> AromaCellSequenceFile:
> >> >> Name: GenomeWideSNP_6
> >> >> Tags: HB20080710
> >> >> Full name: GenomeWideSNP_6,HB20080710
> >> >> Pathname:
> >> >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs
> >> >> File size: 170.92 MB (179217531 bytes)
> >> >> RAM: 0.00 MB
> >> >> Number of data rows: 6892960
> >> >> File format: v1
> >> >> Dimensions: 6892960x26
> >> >> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> >> >> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
> >> >> raw
> >> >> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> >> >> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
> >> >> Footer: <createdOn>20080710 22:47:02
> >> >> PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</ch
> >> >>
> >> >> ipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341
> >> >>
> >> >> 479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></src
> >> >>
> >> >> File><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>9
> >> >> 6968290</filesize>
> >> >> <checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2>
> >> >> Chip type: GenomeWideSNP_6
> >> >> Platform: Affymetrix> getChecksum(acs)
>
> >> >> [1] "f04f081e0a1900653d957a8f320744c0"
>
> >> >> FYI, it is one of the internal sanity checks that catches the error.
> >> >> We've never experienced this ourselves and we've processed thousands
> >> >> of GenomeWideSNP_6 arrays. There is probably a simple answer to this.
>
> >> >> /Henrik
>
> >> >> On Tue, Aug 30, 2011 at 12:14 AM, DGoode <dgoode.stanf...@gmail.com>
> >> >> wrote:
> >> >> > Hi Henrik. Thanks for your reply.
>
> >> >> > The output of sessionInfo() is below, after the output of the call to
> >> >> > process().
>
> >> >> > Cheers,
> >> >> > David
>
> >> >> >> csC <- process(acc, verbose=verbose)
> >> >> > Calibrating data set for allelic cross talk...
> >> >> > Compressing model parameter to a short format...
> >> >> > Compressing model parameter to a short format...done
> >> >> > Calibrating 4 arrays...
> >> >> > Path: probeData/Test,set,Data,ACC,ra,-XY/GenomeWideSNP_6
> >> >> > Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of
> >> >> > 4...
> >> >> > Error: length(pos) == ncol(cells) is not TRUE
> >> >> > Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of
> >> >> > 4...done
> >> >> > Calibrating 4 arrays...done
> >> >> > Calibrating data set for allelic cross talk...done
>
> >> >> >> sessionInfo()
> >> >> > R version 2.13.1 (2011-07-08)
> >> >> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> >> >> > locale:
> >> >> > [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
>
> >> >> > attached base packages:
> >> >> > [1] stats graphics grDevices datasets utils methods
> >> >> > base
>
> >> >> > other attached packages:
> >> >> > [1] aroma.affymetrix_2.1.6 affxparser_1.24.0
> >> >> > aroma.apd_0.2.0
> >> >> > [4] R.huge_0.3.0 aroma.core_2.1.4
> >> >> > aroma.light_1.20.0
> >> >> > [7] matrixStats_0.2.2 R.rsp_0.6.2
> >> >> > R.cache_0.4.3
> >> >> > [10] R.filesets_1.1.0 digest_0.5.0
> >> >> > R.utils_1.7.8
> >> >> > [13] R.oo_1.8.1 R.methodsS3_1.2.1
>
> >> >> > On Aug 28, 10:05 am, Henrik Bengtsson <henrik.bengts...@aroma-
> >> >> > project.org> wrote:
> >> >> >> Hi,
>
> >> >> >> could you please us know what your sessionInfo() reports after
> >> >> >> library(aroma.affymetrix) is called, or even, better after you get
> >> >> >> the
> >> >> >> error? That will be key to troubleshooting this.
>
> >> >> >> /Henrik
>
> >> >> >> On Wed, Aug 24, 2011 at 11:00 PM, DGoode <dgoode.stanf...@gmail.com>
> >> >> >> wrote:
> >> >> >> > Hi, I'm a new user of aroma.affymetrix. I run into a problem
> >> >> >> > immediately after the allele crosstalk calibration step. I get the
> >> >> >> > cryptic error "Error: length(pos) == ncol(cells) is not TRUE", but
> >> >> >> > I
> >> >> >> > can't seem to access the 'pos' or 'cells' variables.
>
> >> >> >> > I successfully completed all of the steps for CRMA v2 with a
> >> >> >> > smaller
> >> >> >> > data set but now I always encounter this problem.
>
> >> >> >> > Could someone please tell me what I might be overlooking or doing
> >> >> >> > wrong? I haven't had any luck searching the group.
>
> >> >> >> > Thanks!
>
> >> >> >> > David
>
> >> >> >> >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6",
> >> >> >> >> tags="Full")
> >> >> >> >> csNorms <-
>
> ...
>
> read more »
--
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