Hi, I leave this one to Mark Robinson who is designed createUniqueCdf() for AffymetrixCdfFile and is on top of this. Though, in the meanwhile could you please:
1. Clarify the origin of Mm_PromPR_v02.CDF, because Affymetrix does not provide an CDF. 2. Make the Mm_PromPR_v02.CDF available to us? If you're happy to share it (and got the rights), I'm happy to have aroma-project.org to either link to it or host it. /Henrik On Fri, Mar 12, 2010 at 8:04 PM, stvjc <carey...@gmail.com> wrote: >> 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 -- 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
