exonmap problems with rma normalization
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Last seen 8.4 years ago
Hi, I got several .CEL files to do RMA using exonmap library below: library(exonmap) library(xmapcore) library(exon.pmcdf) raw.data<-read.exon(covdesc="covdesc") raw.data at cdfName<-"exon.pmcdf"# which CDF file defines the array by setting the name of the .cdf #RMA normalization and generate probeset summaries x.rma<-rma(raw.data) The problem is that at this point i got an error message: Attaching package: 'exon.pmcdf' The following object(s) are masked from 'package:hugene10stv1cdf': i2xy, xy2i Error in .local(object, ...) : subscript out of bounds This is my session info sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-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] stats graphics grDevices utils datasets methods base other attached packages: [1] exon.pmcdf_1.1 hugene10stv1cdf_2.8.0 exonmap_1.0.07 [4] plier_1.22.0 RMySQL_0.7-5 DBI_0.2-5 [7] RColorBrewer_1.0-2 simpleaffy_2.28.0 gcrma_2.24.1 [10] genefilter_1.34.0 affy_1.30.0 Biobase_2.12.1 loaded via a namespace (and not attached): [1] affyio_1.20.0 annotate_1.30.0 AnnotationDbi_1.14.1 [4] Biostrings_2.20.0 IRanges_1.10.0 preprocessCore_1.14.0 [7] RSQLite_0.9-4 splines_2.13.0 survival_2.36-8 [10] tools_2.13.0 xtable_1.5-6 this is my raw data AffyBatch object size of arrays=1050x1050 features (21 kb) cdf=exon.pmcdf (1411189 affyids) number of samples=12 number of genes=1411189 annotation=hugene10stv1 notes= and this is my covdesc file group IG100120JMI046-3gst_01.CEL a IG100120JMI045-3gst_01.CEL a IG100120JMI044-3gst_01.CEL a IG100120JMI043-3gst_01.CEL a IG100120JMI042-3gst_01.CEL a IG100120JMI041-3gst_01.CEL a IG100120JMI040-3gst_01.CEL b IG100120JMI039-3gst_01.CEL b IG100120JMI038-3gst_01.CEL b IG100120JMI037-3gst_01.CEL b IG100120JMI036-3gst_01.CEL b IG100120JMI035-3gst_01.CEL b Can You help me please??? Thanks in advance PS: i tried t
Normalization cdf exonmap Normalization cdf exonmap • 663 views

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