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
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--
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