Question: PGSEA and smcPlot
0
gravatar for Iain Gallagher
8.3 years ago by
United Kingdom
Iain Gallagher930 wrote:
Hi List I'm using PGSEA and I would like to plot the results of my analysis using the smcPlot function in the package. Using this function appends a row labelled 'GS' at the bottom of the plot. I would like to use custom row labels for my plot and have created a vector of names as suggested in the package documentation. When I try to use this I get the following error: Error in axis(4, 1:nrow(m), las = 2, line = -0.5, tick = 0, labels = rnames, : 'at' and 'labels' lengths differ, 52 != 51 suggesting that my rnames vector and the number of rows in the matrix used for the plot have different lengths. They don't however - both are 51. The 'GS' not in the matrix before it goes into the plotting function (smcPlot) and I can't see anything indicating that this is added in the plotting function. I've also tried adding a 'dummy' label to my vector of row labels (i.e. to make it 52 in length) but the result is the same. Could anyone enlighten me? Thanks iain > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pheatmap_0.3 limma_3.6.6 PGSEA_1.14.0 [4] samr_1.28 impute_1.26.0 GOstats_2.18.0 [7] graph_1.30.0 Category_2.16.0 genefilter_1.32.0 [10] hgu133plus2.db_2.4.5 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 [13] DBI_0.2-5 annotate_1.28.0 AnnotationDbi_1.14.1 [16] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 colorspace_1.0-1 GO.db_2.5.0 [4] grid_2.13.1 GSEABase_1.12.1 preprocessCore_1.12.0 [7] RBGL_1.28.0 splines_2.13.1 survival_2.36-9 [10] tools_2.13.1 XML_3.4-0 xtable_1.5-6 >
go hgu133plus2 pgsea • 575 views
ADD COMMENTlink written 8.3 years ago by Iain Gallagher930
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