Hi,
start by updating to the latest version,
and see if that solves it. I've just verified that it works with
aroma.affymetrix v2.5.0:
> library("aroma.affymetrix");
> verbose <- Arguments$getVerbose(-50, timestamp=TRUE);
> dataSetName <- "Affymetrix_2011-CytoScanHD";
> chipType <- "CytoScanHD_Array";
> cdf <- AffymetrixCdfFile$byChipType(chipType);
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
Filesize: 612.27MB
Chip type: CytoScanHD_Array
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4
> getFileSize(cdf)
[1] 642007896
> getChecksum(cdf)
[1] "20e3bf19b08c520bc8c348fea00c3f3d"
> acs <- getAromaCellSequenceFile(cdf)
> acs
AromaCellSequenceFile:
Name: CytoScanHD_Array
Tags: HB20111008
Full name: CytoScanHD_Array,HB20111008
Pathname:
annotationData/chipTypes/CytoScanHD_Array/CytoScanHD_Array,HB20111008.acs
File size: 170.92 MB (179217487 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>20111108 21:44:22
PST</createdOn><platform>Affymetrix</platform><chipType>CytoScanHD_Array</chipType><srcFile><filename>CytoScanHD_Array.probe_tab</filename><filesize>409176930</filesize><checksum>beaaa56413608b3f9d9d464a07cddcae</checksum></srcFile><createdBy><fullname>Henrik
Bengtsson</fullname><email>henrik.bengts...@aroma-project.org</email></createdBy>
Chip type: CytoScanHD_Array
Platform: Affymetrix
> csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf);
> dsList <- doASCRMAv2(csR, verbose=verbose);
[...]
20120410 15:01:39| Chunk #20 of 21...
20120410 15:01:39| Elements:
int [1:100000] 2701512 2701513 2701514 2701515 2701516 2701517 27015
18 2701519 2701520 2701521 ...
20120410 15:01:39| Querying CDF file...
20120410 15:01:41| Querying CDF file...done
20120410 15:01:41| Restructuring...
20120410 15:01:41| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1345324 71.9 2134030 114.0 27465550 1466.9
Vcells 20369379 155.5 29844431 227.7 55707687 425.1
20120410 15:01:41| Chunk #20 of 21...done
20120410 15:01:41| Chunk #21 of 21...
20120410 15:01:41| Elements:
int [1:20614] 2801512 2801513 2801514 2801515 2801516 2801517 280151
8 2801519 2801520 2801521 ...
20120410 15:01:41| Querying CDF file...
20120410 15:01:42| Querying CDF file...done
20120410 15:01:42| Restructuring...
20120410 15:01:42| Restructuring...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 630851 33.7 2134030 114.0 27465550 1466.9
Vcells 19615212 149.7 29844431 227.7 55707687 425.1
20120410 15:01:42| Chunk #21 of 21...done
20120410 15:01:42| lapplyInChunks()...done
20120410 15:01:42| Reading cell indices from CDF file...done
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 445167 23.8 1707224 91.2 27465550 1466.9
Vcells 17398676 132.8 29844431 227.7 55707687 425.1
20120410 15:01:42| readUnits.AffymetrixCdfFile(): Updating cache
20120410 15:01:42| Non-SNP cells:...
int [1:2037534] 6344052 5132417 3744071 1409905 879528 5837958 5341975
4106306 1391737 1201593 ...
20120410 15:01:42| Non-SNP cells:...done
[...]
> sessionInfo()
R version 2.15.0 Patched (2012-04-08 r58935)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_2.5.1 affxparser_1.27.5 aroma.apd_0.2.2
[4] R.huge_0.3.0 aroma.core_2.5.0 aroma.light_1.23.1
[7] matrixStats_0.4.4 R.rsp_0.7.5 R.cache_0.6.2
[10] R.filesets_1.1.5 digest_0.5.2 R.utils_1.13.0
[13] R.oo_1.9.4 R.methodsS3_1.2.2
loaded via a namespace (and not attached):
[1] tools_2.15.0
Make sure that your CDF is the same as mine (it may be that you're
sitting on an early-access version - hope I'm not). Also make sure
your ACS file (see above) is the same/correct.
/Henrik
On Tue, Apr 10, 2012 at 7:47 AM, Mike
<michael.wal...@med.uni-tuebingen.de> wrote:
> Dear List,
>
> I used aroma.affymetrix successfully to analyze Affy 6.0 SNP arrays. Now, we
> moved to CytoScanHD arrays and I wanted to do the same analysis (paired
> tumor-normal copy number analysis). I found the cdf and annotation files
> stated below (the link now is
> http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/).
> When I try analyze my CEL files (which are in the folder
> "rawData\CytoScan_Workshop\CytoScanHD_Array" using the code below, get an
> error message from the doCRMAv2() call. Any help would be highly
> appreciated.
>
> Thank you very much in advance,
>
> Mike
>
> Here is the code I used, ...
>
> library("aroma.affymetrix")
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> options(digits=4)
> chipType <- "CytoScanHD_Array";
> cdf <- AffymetrixCdfFile$byChipType(chipType);
> dataSet <- "CytoScan_Workshop";
> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
>
>
> ... which leads to this error:
>
> Error in readCdfCellIndices(pathname, ...) :
> Argument 'units' contains an element out of range: 2822126
> 20120410 16:45:38| Querying CDF file...done
> 20120410 16:45:38| Chunk #21 of 21...done
> 20120410 16:45:38| lapplyInChunks()...done
> 20120410 16:45:38| Reading cell indices from CDF file...done
> 20120410 16:45:38| Non-SNP units:...done
> 20120410 16:45:38| Identifying cell indices for all non-SNP
> units...done
> 20120410 16:45:38| Identifying sets of pairs of cell indices...done
> 20120410 16:45:38| Array #1 ('M12D002a01') of 11...done
> 20120410 16:45:38| Calibrating 11 arrays...done
> 20120410 16:45:38| Calibrating data set for allelic cross talk...done
>
>
> sessionInfo()
>
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
> LC_MONETARY=German_Germany.1252
> [4] LC_NUMERIC=C LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.4.0 affxparser_1.26.4 aroma.apd_0.2.0
> R.huge_0.3.0
> [5] aroma.core_2.4.6 aroma.light_1.22.0 matrixStats_0.4.4
> R.rsp_0.7.3
> [9] R.cache_0.6.1 R.filesets_1.1.4 digest_0.5.2
> R.utils_1.12.0
> [13] R.oo_1.9.3 R.methodsS3_1.2.2
>
>
>
> Am Freitag, 6. Januar 2012 14:44:00 UTC+1 schrieb Henrik Bengtsson:
>>
>> Hi David,
>>
>> I've created ACS, UFL and UGP files for the CytoScanHD_Array chip type,
>> but they are still to be validated. You could start by comparing the
>> content of yours to mine, which you find at:
>>
>>
>> http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/incomplete/
>>
>> /Henrik
>>
>> On Thursday, January 5, 2012, D Goode wrote:
>>>
>>> OK, I think I worked it out. I've created UFL & UPG files for the
>>> CytoScan HD and am working on building an ACS file.
>>>
>>> Can anyone recommend some sanity checks I could carry out to make sure I
>>> did this properly? Everything seems fine when I double-check the data for a
>>> few randomly selected probes.
>>>
>>> Cheers,
>>> David
>>>
>>> --
>>> 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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>
> --
> 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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