Hi again, On Sat, Aug 27, 2011 at 5:22 PM, Henrik Bengtsson <henrik.bengts...@aroma-project.org> wrote: > 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.
This problems still remains - so I'm still interested in an example CEL file. About your other problem - the error "length(pos) == ncol(cells) is not TRUE" - it has been fixed. Please see my reply on Aug 30, 2011 to thread 'Re: [aroma.affymetrix] Re: problem processing output of AllelicCrosstalkCalibration': https://groups.google.com/forum/#!topic/aroma-affymetrix/nVjEFHoORAw for details. The solution is to update. Thanks for reporting on this problem. Cheers, Henrik > > /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. 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/
