Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
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: createdOn20080710 22:47:02
PDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6/chipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/filenamefilesize341479928/filesizechecksum2037c033c09fd8f7c06bd042a77aef15/checksum/srcFilesrcFile2filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize96968290/filesize
checksum3dc2d3178f5eafdbea9c8b6eca88a89c/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$byName(Normal,TCGA,controls,and,778,Data,
cdf=cdf)
print(csNorms)
AffymetrixCelSet:
Name: Normal
Tags: TCGA,controls,and,778,Data
Path: rawData/Normal,TCGA,controls,and,778,Data/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
Number of arrays: 29
Names: COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042,
COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G07_293052,
COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G09_293056, ...,
TOUSE_p_TCGAaffxB9_10a_N_GenomeWideSNP_6_E05_397070 [29]
Time period: 2008-07-12 15:05:45 -- 2009-04-01 23:50:47
Total file size: 1910.19MB
RAM: 0.03MB
accNorms - AllelicCrosstalkCalibration(csNorms, model=CRMAv2)
print(accNorms)
AllelicCrosstalkCalibration:
Data set: Normal
Input tags:
Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration
Hi.
On Tue, Aug 30, 2011 at 5:45 PM, DGoode dgoode.stanf...@gmail.com wrote:
Hi Henrik,
I think I got the same output you did - but I've pasted it below for
you to check if you'd like.
Running diff only turned up differences in spacing at the end of
lines.
Ok.
I'm running Lion (OS X 10.7.1). Could that be contributing to the
problem?
I don't think so.
Could you make your
'COTES_p_TCGAaffxB8_9a_S_GenomeWideSNP_6_G02_293042.CEL' file
available to me so I can try to reproduce it myself? Please gzip it.
BTW, if you do
df - getFile(csR, 1);
print(df);
what do you get? It should show the above CEL file - if not use
another index for getFile().
/Henrik
Thanks,
David
##
cdf - AffymetrixCdfFile$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: createdOn20080710 22:47:02
PDT/createdOnplatformAffymetrix/
platformchipTypeGenomeWideSNP_6/
chipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/
filenamefilesize341479928/filesize
checksum2037c033c09fd8f7c06bd042a77aef15/checksum/
srcFilesrcFile2
filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize96968290/
filesize
checksum3dc2d3178f5eafdbea9c8b6eca88a89c/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: createdOn20080710 22:47:02
PDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6/ch
ipTypesrcFilefilenameGenomeWideSNP_6.probe_tab/filenamefilesize341
479928/filesizechecksum2037c033c09fd8f7c06bd042a77aef15/checksum/src
FilesrcFile2filenameGenomeWideSNP_6.CN_probe_tab/filenamefilesize9
6968290/filesize
checksum3dc2d3178f5eafdbea9c8b6eca88a89c/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) ==
