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 <-
>> >> >> >> AffymetrixCelSet$byName("Normal,TCGA,controls,and,778,Data",
>> >> >> >> cdf=cdf)
>>
>> >> >> >> print(csNorms)
>> >> >> > AffymetrixCelSet:
>> >> >> > Name: Normal
>> >> >> > Tags: TCGA,controls,and,778,Data
>> >> >> > Path: rawData/Normal,TCGA,controls,and,778,Data/GenomeWideSNP_6
>> >> >> > Platform: Affymetrix
>> >> >> > Chip type: GenomeWideSNP_6,Full
>> >> >> > Number of arrays: 29
>> >> >> > Names: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042,
>> >> >> > COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G07_293052,
>> >> >> > COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G09_293056, ...,
>> >> >> > TOUSE_p_TCGAaffxB9_10a_N_GenomeWideSNP_6_E05_397070 [29]
>> >> >> > Time period: 2008-07-12 15:05:45 -- 2009-04-01 23:50:47
>> >> >> > Total file size: 1910.19MB
>> >> >> > RAM: 0.03MB
>>
>> >> >> >> accNorms <- AllelicCrosstalkCalibration(csNorms, model="CRMAv2")
>> >> >> >> print(accNorms)
>> >> >> > AllelicCrosstalkCalibration:
>> >> >> > Data set: Normal
>> >> >> > Input tags: TCGA,controls,and,778,Data
>> >> >> > User tags: *
>> >> >> > Asterisk ('*') tags: ACC,ra,-XY
>> >> >> > Output tags: TCGA,controls,and,778,Data,ACC,ra,-XY
>> >> >> > Number of files: 29 (1910.19MB)
>> >> >> > Platform: Affymetrix
>> >> >> > Chip type: GenomeWideSNP_6,Full
>> >> >> > Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200,
>> >> >> > subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr
>> >> >> > "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075
>> >> >> > 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98)
>> >> >> > Output path: probeData/Normal,TCGA,controls,and,778,Data,ACC,ra,-XY/
>> >> >> > GenomeWideSNP_6
>> >> >> > Is done: FALSE
>> >> >> > RAM: 0.01MB
>>
>> >> >> >> csC.Norms <- process(accNorms, 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 29 arrays...
>> >> >> > Path: probeData/Normal,TCGA,controls,and,778,Data,ACC,ra,-XY/
>> >> >> > GenomeWideSNP_6
>> >> >> > Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of
>> >> >> > 29...
>> >> >> > Error: length(pos) == ncol(cells) is not TRUE
>> >> >> > Array #1 ('COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042') of
>> >> >> > 29...done
>> >> >> > Calibrating 29 arrays...done
>> >> >> > Calibrating data set for allelic cross talk...done
>> >> >> > Execution halted
>>
>> >> >> > --
>> >> >> > 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
>>
>> ...
>>
>> read more »
>
> --
> 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
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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.
You received this message because you are subscribed to the Google Groups
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