Dear list, I am using aroma.affymetrix to normalize GenomeWideSNP_6 data. I have setup the library and CEL files as described on the website.
When I am trying to execute the following block... acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2"); print(acc); cs.C <- process(acc, verbose=log); print(cs.C); I get the following error while processing the first sample: 20110607 19:01:08| Fitting...done 20110607 19:01:08| Allele probe-pair group #7 ('missing') of 7...done 20110607 19:01:08| Fitting calibration model...done 20110607 19:01:08| Estimated origins: A/C A/G A/T C/G C/T G/T missing A 129.1 153.8 132.8 165.0 213.2 136.1 141 B 139.9 113.2 107.6 117.5 160.6 149.1 137 20110607 19:01:08| Weighted average offset: 153.30 20110607 19:01:08| Backtransforming (calibrating) data... 20110607 19:01:08| Allele basepair #1 ('A/C') of 7... 20110607 19:01:08| Allele basepair #1 ('A/C') of 7...done 20110607 19:01:08| Allele basepair #2 ('A/G') of 7... 20110607 19:01:08| Allele basepair #2 ('A/G') of 7...done 20110607 19:01:08| Allele basepair #3 ('A/T') of 7... 20110607 19:01:09| Allele basepair #3 ('A/T') of 7...done 20110607 19:01:09| Allele basepair #4 ('C/G') of 7... 20110607 19:01:09| Allele basepair #4 ('C/G') of 7...done 20110607 19:01:09| Allele basepair #5 ('C/T') of 7... 20110607 19:01:09| Allele basepair #5 ('C/T') of 7...done 20110607 19:01:09| Allele basepair #6 ('G/T') of 7... 20110607 19:01:10| Allele basepair #6 ('G/T') of 7...done 20110607 19:01:10| Allele basepair #7 ('missing') of 7... 20110607 19:01:10| Allele basepair #7 ('missing') of 7...done 20110607 19:01:10| Backtransforming (calibrating) data...done 20110607 19:01:10| Correcting offset for all non-SNP cells... 20110607 19:01:10| Cells: int [1:964281] 3466656 3466655 3463975 3463976 3461296 3461295 3458616 3458615 3455936 3455935 ... 20110607 19:01:10| Offset: 153.301161350039 20110607 19:01:10| Correcting offset for all non-SNP cells...done Error in rescale(this, yAll = yAll, params = params, setsOfProbes = setsOfProbes, : unused argument(s) (yAll = yAll, params = params, setsOfProbes = setsOfProbes, verbose = less(verbose)) 20110607 19:01:10| Array #1 ('37A55') of 46...done 20110607 19:01:10| Calibrating 46 arrays...done 20110607 19:01:10|Calibrating data set for allelic cross talk...done Then the script halts. I tried using the doCRMAv2 wrapper, with the same result. I tried using another dataset, and got the same error. I also tried re-installing aroma.affymetrix and aroma.cn. > hbInstall("aroma.affymetrix") > hbInstall("aroma.cn") (I do not get this error while analyzing Mapping250K_{Nsp,Sty} data with a similar script.) > aroma.affymetrix [1] "AromaAffymetrix: aroma.affymetrix v2.1.0 (2011-04-08) is loaded (pos=9). > aroma.cn [1] "Package: aroma.cn v0.5.2 (2010-08-04) is loaded (pos=2). > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-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] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] aroma.cn_0.5.2 sfit_0.2.0 bioinf_1.0 [4] ggplot2_0.8.9 proto_0.3-8 reshape_0.8.4 [7] plyr_1.4 aroma.affymetrix_2.1.0 aroma.apd_0.1.8 [10] affxparser_1.22.1 R.huge_0.2.2 aroma.core_2.1.0 [13] aroma.light_1.20.0 matrixStats_0.2.2 R.rsp_0.5.3 [16] R.cache_0.4.2 R.filesets_1.0.1 digest_0.5.0 [19] R.utils_1.7.5 R.oo_1.8.0 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] tools_2.13.0 -- 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/