Hi, seeing these error messages, my best guess is that those CEL files with DAT headers containing only ".1sq" instead of the expected "GenomeWideSNP_6.1sq" are somehow corrupt and not real GenomeWideSNP_6 CEL files. To be sure I need to study such a file. Would you mind making one of the ".1sq" CEL files available (ftp, website, ...) and I'll have a look at it.
/Henrik On Fri, Aug 26, 2011 at 8:52 AM, Irina Ostrovnaya <rishe...@gmail.com> wrote: > Hi, > I'm encountering two errors: > 1) error happens with: > cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf); > print(cs) > Error in if (hasTimestamp) { : argument is of length zero > > It seems that samples that go through have: > getHeader(getFile(cs, 1))$datheader > [1] "[0..65534] D1_GenomeWideSNP_6:CLS=20508RWS=20508XIN=0 YIN=0 > VE=0 0 12/10/10 12:05:43 50205130 M10 \024 \024 > GenomeWideSNP_6.1sq \024 \024 \024 \024 \024 570 \024 25565.199219 > \024 3.500000 \024 0.7000 \024 3" > > And samples that don't go through have something like: > getHeader(getFile(cs, 5))$datheader > [1] "[2..65534] > D2_plus_D1785_GenomeWideSNP_6:CLS=20491RWS=20491XIN=0 YIN=0 > VE=0 0 12/09/10 01:52:21 50205130 M10 \024 \024 .1sq > \024 \024 \024 \024 \024 570 \024 25556.708984 \024 3.500000 \024 > 0.7000 \024 3" > > > If I get rid of samples that have .1sq instead of GenomeWideSNP_6.1sq, > everything works > > 2) > then I encounter the second problem with process(acc, > verbose=verbose), reported by DGoode as well > Error: length(pos) == ncol(cells) is not TRUE > > > 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 61 arrays... > Path: probeData/data,ACC,ra,-XY/GenomeWideSNP_6 > Array #1 ('DC_D1123_GenomeWideSNP_6') of 61... > Identifying sets of pairs of cell indices... > Chip type: GenomeWideSNP_6,Full > Merge shifts: TRUE > Number of nucleotides: 1 > Locating AromaCellSequenceFile... > Chip type: GenomeWideSNP_6 > Number of cells: 6892960 > 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 > Locating AromaCellSequenceFile...done > Identifying cell indices for all non-SNP units... > Non-SNP units:... > int [1:946447] 1 2 3 4 5 6 7 8 9 10 ... > Reading cell indices from CDF file... > Pathname: annotationData/chipTypes/GenomeWideSNP_6/ > GenomeWideSNP_6,Full.cdf > Units: > int [1:946447] 1 2 3 4 5 6 7 8 9 10 ... > lapplyInChunks()... > Number of elements per chunk: 1e+05 > Chunk #1 of 10... > ... > Identifying SNP positions of cell allele pairs... > Checking for cached results... > Found cached results > Checking for cached results...done > Identifying SNP positions of cell allele pairs...done > SNP positions: > int [1:2916605] 10 10 10 11 11 11 11 11 11 16 ... > Error: length(pos) == ncol(cells) is not TRUE > Retrieving SNP nucleotides...done > Get SNP nucleotide sequence pairs...done > Identifying groups of SNP nucleotide sequence pairs...done > Non-SNP units:...done > Identifying cell indices for all non-SNP units...done > Identifying sets of pairs of cell indices...done > Array #1 ('DC_D1123_GenomeWideSNP_6') of 61...done > Calibrating 61 arrays...done > Calibrating data set for allelic cross talk...done > >> print(csC); > Error in print(csC) : object 'csC' not found > > > sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] ACNE_0.4.3 MASS_7.3-13 > aroma.affymetrix_2.1.6 > [4] affxparser_1.24.0 aroma.apd_0.2.0 R.huge_0.3.0 > [7] aroma.core_2.1.4 aroma.light_1.20.0 matrixStats_0.2.2 > [10] R.rsp_0.6.2 R.cache_0.4.3 R.filesets_1.1.0 > [13] digest_0.5.0 R.utils_1.7.8 R.oo_1.8.1 > [16] R.methodsS3_1.2.1 > > > Any recommendations? > Thanks! > > -- > 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. 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