Thank you Valerie and Loyal. That was helpful. Adrian On Tue, Mar 5, 2013 at 11:24 PM, Loyal Goff <lgoff at="" csail.mit.edu=""> wrote: > To follow up, there also exists an fpkmMatrix() method to reshape the fpkm results into a feature X condition matrix, e.g.: > > fpkmMatrix(myGenes) > > Cheers, > Loyal > > On Mar 5, 2013, at 11:17 PM, Valerie Obenchain <vobencha at="" fhcrc.org=""> wrote: > >> Hi Adrian, >> >> If we follow the example in the vignette we eventually get to these lines which I think are similar to what you are showing below. >> >> From vignette: >> ... >> >> data(sampleData) >> myGeneIds<-sampleIDs >> myGeneIds >> myGenes<-getGenes(cuff,myGeneIds) >> myGenes >> head(fpkm(myGenes)) >> h<-csHeatmap(myGenes,cluster='both') >> >> >> To get the data plotted in csHeatmap() you'll want to look inside the the 'myGenes' object. >> >> > myGenes >> CuffGeneSet instance for 20 genes >> >> Slots: >> annotation >> fpkm >> repFpkm >> diff >> count >> isoforms CuffFeatureSet instance of size 45 >> TSS CuffFeatureSet instance of size 23 >> CDS CuffFeatureSet instance of size 36 >> promoters CuffFeatureSet instance of size 20 >> splicing CuffFeatureSet instance of size 23 >> relCDS CuffFeatureSet instance of size 20 >> >> Each of the slots has an accessor and I think fpkm() is what your are looking for. >> >> > head(fpkm(myGenes)) >> gene_id sample_name fpkm conf_hi conf_lo quant_status >> 1 XLOC_000069 Fibroblasts 2.05083e-01 8.94501e-01 0.000 OK >> 2 XLOC_000069 hESC 1.77686e+02 2.15888e+02 139.484 OK >> 3 XLOC_000069 iPS 1.90000e+01 3.88149e+01 0.000 OK >> 4 XLOC_000089 Fibroblasts 1.39701e+04 2.19187e+04 6021.450 OK >> 5 XLOC_000089 hESC 7.18339e+03 7.92296e+03 6443.810 OK >> 6 XLOC_000089 iPS 1.41690e+03 1.96558e+03 868.215 OK >> stdev >> 1 0.344709 >> 2 19.101000 >> 3 9.907450 >> >> >> Valerie >> >> >> On 03/01/13 10:05, Adrian Johnson wrote: >>> Hi: >>> I am trying to plot the most significant genes. I have 3 different >>> sample types and 4 replicates each. Could anyone suggest how do I get >>> the matrix of fpkm values that was plotted in csHeatmap function. >>> >>>> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.001) >>>> diffGenes<-getGenes(cuff,diffGeneIDs) >>>> h<-csHeatmap(diffGenes,cluster='both') >>> >>> the heatmap gene names are not visible. I want to get the matrix for h >>> and plot heatmap using another heatmap function. >>> How do I get the matrix for h. >>> >>> thanks >>> Adrian >>> >>> >>> >>> >>> >>> >>> >>> >>>> sessionInfo() >>> R version 2.15.2 (2012-10-26) >>> Platform: i386-w64-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >>> States.1252 LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_United >>> States.1252 >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 >>> GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.8 >>> reshape2_1.2.2 >>> [8] ggplot2_0.9.3 RSQLite_0.11.2 DBI_0.2-5 >>> BiocGenerics_0.4.0 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.20.4 Biobase_2.18.0 biomaRt_2.14.0 >>> Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 >>> [7] BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-1 >>> dichromat_2.0-0 digest_0.6.3 >>> GenomicFeatures_1.10.2 >>> [13] gtable_0.1.2 Hmisc_3.10-1 labeling_0.1 >>> lattice_0.20-13 MASS_7.3-23 munsell_0.4 >>> [19] parallel_2.15.2 plyr_1.8 proto_0.3-10 >>> RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2 >>> [25] scales_0.2.3 stats4_2.15.2 stringr_0.6.2 >>> tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >