Question: CHARM - The following columns in sampleKey...
7.0 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hello I've being trying to get charm to read in some Nimblegen array data that I had to convert from PAIR to XYS, also making an annotation file. All goes swimmingly, until I try to use readCharm, although the data appears to load, I get the following error when using readCharm: The following columns in sampleKey contain discrepant values between channels and are being removed: 1 It's not clear what this means, as I have looked at the two channel files (532 and 635) and the structure is essentially the same. Subsequent analyses fail, I assume because of missing data. If I look at my loaded dataset with rawData I get the following: > rawData TilingFeatureSet (storageMode: lockedEnvironment) assayData: 389307 features, 39 samples element names: channel1, channel2 protocolData rowNames: N3 N9 ... E2 (39 total) varLabels: filenamesChannel1 filenamesChannel2 dates1 dates2 varMetadata: labelDescription channel phenoData rowNames: N3 N9 ... E2 (39 total) varLabels: sampleID tissue arrayUT arrayMD varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.2006.11.02.hg18.cpg.promo Can anyone help? -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale:  LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C  LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8  LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  pd.2006.11.02.hg18.cpg.promo_0.0.1 oligo_1.22.0  oligoClasses_1.20.0 RSQLite_0.11.2  DBI_0.2-5 charm_2.4.0  genefilter_1.40.0 RColorBrewer_1.0-5  fields_6.7 spam_0.29-2  SQN_1.0.5 nor1mix_1.1-3  mclust_4.0 Biobase_2.18.0  BiocGenerics_0.4.0 loaded via a namespace (and not attached):  affxparser_1.30.0 affyio_1.26.0 annotate_1.36.0  AnnotationDbi_1.20.2 BiocInstaller_1.8.3 Biostrings_2.26.2  bit_1.1-9 BSgenome_1.26.1 codetools_0.2-8  corpcor_1.6.4 ff_2.2-9 foreach_1.4.0  GenomicRanges_1.10.3 gtools_2.7.0 IRanges_1.16.3  iterators_1.0.6 limma_3.14.1 MASS_7.3-22  multtest_2.14.0 parallel_2.15.2 preprocessCore_1.20.0  siggenes_1.32.0 splines_2.15.2 stats4_2.15.2  survival_2.36-14 sva_3.4.0 XML_3.95-0.1  xtable_1.7-0 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
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