> cdfU AffymetrixCdfFile: Path: annotationData/chipTypes/Mm_PromPR_v02 Filename: Mm_PromPR_v02,unique.CDF Filesize: 126.33MB Chip type: Mm_PromPR_v02,unique RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 3026x3026 Number of cells: 9156676 Number of units: 25373 Cells per unit: 360.88 Number of QC units: 0 > cdf AffymetrixCdfFile: Path: annotationData/chipTypes/Mm_PromPR_v02 Filename: Mm_PromPR_v02.cdf Filesize: 126.33MB Chip type: Mm_PromPR_v02 RAM: 0.00MB File format: v4 (binary; XDA) Dimension: 2166x2166 Number of cells: 4691556 Number of units: 25373 Cells per unit: 184.90 Number of QC units: 0
this leads to (i think) > csU = convertToUnique(csN, verbose=verbose) 20100312 14:02:59|Converting to unique CDF... 20100312 14:02:59| Getting unique CDF... 20100312 14:02:59| Getting unique CDF...done 20100312 14:02:59| Input tags:MN,lm 20100312 14:02:59| Input Path: probeData/Dawn,MN,lm/Mm_PromPR_v02 20100312 14:02:59| Output Path:probeData/Dawn,MN,lm,UNQ/Mm_PromPR_v02 20100312 14:02:59| allTags:MN,lm,UNQ 20100312 14:02:59| Test whether dataset exists 20100312 14:02:59| Reading cell indices from standard CDF... 20100312 14:03:08| Reading cell indices from standard CDF...done 20100312 14:03:08| Reading cell indices list from unique CDF... 20100312 14:03:17| Reading cell indices list from unique CDF...done 20100312 14:03:17| Converting CEL data from standard to unique CDF for sample 1 ( 10_BL6_IP_Mmp ) of 8... 20100312 14:03:17| Reading intensity values according to standard CDF... Error in readCel(filename, indices = indices, readHeader = FALSE, readOutliers = FALSE, : Argument 'indices' contains an element out of range. 20100312 14:03:23| Reading intensity values according to standard CDF...done 20100312 14:03:23| Converting CEL data from standard to unique CDF for sample 1 ( 10_BL6_IP_Mmp ) of 8...done 20100312 14:03:23|Converting to unique CDF...done > sessionInfo() R version 2.11.0 Under development (unstable) (2010-03-02 r51194) x86_64-apple-darwin9.8.0 locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] gsmoothr_0.1.4 limma_3.3.4 aroma.affymetrix_1.5.0 [4] aroma.apd_0.1.7 affxparser_1.19.6 R.huge_0.2.0 [7] aroma.core_1.5.0 aroma.light_1.15.1 matrixStats_0.1.9 [10] R.rsp_0.3.6 R.cache_0.2.0 R.filesets_0.8.0 [13] R.utils_1.3.3 R.oo_1.6.7 R.methodsS3_1.1.0 [16] weaver_1.13.0 codetools_0.2-2 digest_0.4.2 -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
