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. >>> >>> >>> 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/ -- 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/