Dear aroma group, I tried to apply CRMAv2 on my 250K_Nsp array data set. The same script ran without problems on another 250K data set a couple of months ago and I can not figure out what is going wrong with my current data set. I downloaded two public CEL files and got the same error. Here are the details:
I used these two CEL files as test data set: wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1241nnn/GSM1241436/suppl/GSM1241436_110830-250K_scc1.CEL.gz wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1241nnn/GSM1241437/suppl/GSM1241437_110830-250K_scc2.CEL.gz My annotationData/chipTypes/Mapping250K_Nsp folder contains these files Mapping250K_Nsp.cdf Mapping250K_Nsp,HB20080710.acs Mapping250K_Nsp,na31,HB20101007.ugp Mapping250K_Nsp,HB20080621,probeSeqs.txt Mapping250K_Nsp,na31,HB20101007.ufl which I obtained from http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/. This is my script and the respective error message: library("aroma.affymetrix") verbose <- Arguments$getVerbose(-8, timestamp=TRUE) Sys.setlocale(locale="C") chipType <- "Mapping250K_Nsp" cdf <- AffymetrixCdfFile$byChipType(chipType) gi <- getGenomeInformation(cdf) si <- getSnpInformation(cdf) acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) csR <- AffymetrixCelSet$byName("testdata", cdf=cdf) print(csR) acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2") print(acc) csC <- process(acc, verbose=verbose) [...] [2014-01-04 16:51:16] Exception: Cannot rescale to target average. After taking the intersect of the subset of cells to be used, there are no cells left. at #06. rescaleByGroups.AllelicCrosstalkCalibration(this, yAll = yAll, params = params, ...) - rescaleByGroups.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #05. rescaleByGroups(this, yAll = yAll, params = params, ...) - rescaleByGroups() is in environment 'aroma.affymetrix' at #04. rescale.AllelicCrosstalkCalibration(this, yAll = yAll, params = params, setsOfProbes = setsOfProbes, verbose = less(verbose)) - rescale.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #03. rescale(this, yAll = yAll, params = params, setsOfProbes = setsOfProbes, verbose = less(verbose)) - rescale() is in environment 'aroma.core' at #02. process.AllelicCrosstalkCalibration(acc, verbose = verbose) - process.AllelicCrosstalkCalibration() is in environment 'aroma.affymetrix' at #01. process(acc, verbose = verbose) - process() is in environment 'aroma.core' Error: Cannot rescale to target average. After taking the intersect of the subset of cells to be used, there are no cells left. In addition: Warning message: In fcn(...) : Packages reordered in search path: package:affxparser 20140104 16:51:16| Array #1 ('GSM1241436_110830-250K_scc1') of 2...done 20140104 16:51:16| Calibrating 2 arrays...done 20140104 16:51:16|Calibrating data set for allelic cross talk...done traceback() 11: stop(cond) 10: throw.Exception(Exception(...)) 9: throw(Exception(...)) 8: throw.default("Cannot rescale to target average. After taking the intersect of the subset of cells to be used, there are no cells left.") 7: throw("Cannot rescale to target average. After taking the intersect of the subset of cells to be used, there are no cells left.") 6: rescaleByGroups.AllelicCrosstalkCalibration(this, yAll = yAll, params = params, ...) 5: rescaleByGroups(this, yAll = yAll, params = params, ...) 4: rescale.AllelicCrosstalkCalibration(this, yAll = yAll, params = params, setsOfProbes = setsOfProbes, verbose = less(verbose)) 3: rescale(this, yAll = yAll, params = params, setsOfProbes = setsOfProbes, verbose = less(verbose)) 2: process.AllelicCrosstalkCalibration(acc, verbose = verbose) 1: process(acc, verbose = verbose) sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=C LC_NUMERIC=C [3] LC_TIME=C LC_COLLATE=C [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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 utils datasets methods base other attached packages: [1] sfit_0.3.0 aroma.light_1.32.0 matrixStats_0.8.12 [4] aroma.affymetrix_2.11.1 aroma.core_2.11.0 R.devices_2.7.2 [7] R.filesets_2.3.0 R.utils_1.28.4 R.oo_1.15.8 [10] affxparser_1.34.0 R.methodsS3_1.5.2 loaded via a namespace (and not attached): [1] DNAcopy_1.36.0 PSCBS_0.40.2 R.cache_0.9.0 R.huge_0.6.0 [5] R.rsp_0.9.28 aroma.apd_0.4.0 digest_0.6.4 tools_3.0.1 Interestingly, the allelic crosstalk calibration works when I set the parameter subsetToAvg=NULL. However, I does not make sense to me why it does not work when probes on chromosomes X and Y were omitted (which is the default). Any help is welcome. Best regards, Hans -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
