gcrma on affy xlaevis arrays
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Last seen 7.1 years ago
Hi I am facing the following problem calling gcrma on an affy X. laevis array. is there a quick solution or do i have to dig deep? tia t. > a AffyBatch object size of arrays=984x984 features (20 kb) cdf=X_laevis_2 (32635 affyids) number of samples=8 number of genes=32635 annotation=xlaevis2 notes= > gcrma(a) Adjusting for optical effect........Done. Computing affinities.Done. Error in sample(1:length(as.matrix(pms)[index.affinities, ]), 25000) : cannot take a sample larger than the population when 'replace = FALSE' > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xlaevis2probe_2.8.0 xlaevis2cdf_2.8.0 arrayQualityMetrics_3.8.0 [4] geneplotter_1.30.0 lattice_0.19-23 annotate_1.30.0 [7] simpleaffy_2.28.0 gcrma_2.24.1 genefilter_1.34.0 [10] annaffy_1.24.0 KEGG.db_2.5.0 GO.db_2.5.0 [13] affy_1.30.0 xlaevis.db_2.5.0 org.Xl.eg.db_2.5.0 [16] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.1 [19] Biobase_2.12.1 loaded via a namespace (and not attached): [1] affyio_1.20.0 affyPLM_1.28.5 beadarray_2.2.0 Biostrings_2.20.0 [5] Cairo_1.4-9 cluster_1.13.3 grid_2.13.0 Hmisc_3.8-3 [9] hwriter_1.3 IRanges_1.10.0 latticeExtra_0.6-14 limma_3.8.1 [13] preprocessCore_1.14.0 RColorBrewer_1.0-2 setRNG_2009.11-1 splines_2.13.0 [17] survival_2.36-5 SVGAnnotation_0.9-0 tools_2.13.0 vsn_3.20.0 [21] XML_3.2-0 xtable_1.5-6 ---------------------------------------------------------------------- Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, M?nchen D
GO affy gcrma GO affy gcrma • 573 views

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