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 Google
>> >> > Groups "aroma.affymetrix" group with
>> >> > websitehttp://www.aroma-project.org/.
>> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> >> > To unsubscribe and other options, go
>> >> > tohttp://www.aroma-project.org/forum/
>>
>> > --
>> > 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 websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
>
> --
> 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-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
