I have been trying to use DEXSeq to do a DEU analysis and plot some of the genes that are coming up in the results. The analysis seems to be working fine (even though I am getting a warning when I estimate the dispersion) and I have about 2000 hits, but when I try to visualise the differences using the plot I get this error:
plotDEXSeq(dxr1, "ENSG00000163660", displayTranscripts=T,legend=TRUE, cex.axis=1.2, cex=1.3, lwd=1) Error in start(unlist(genomicData)) : error in evaluating the argument 'x' in selecting a method for function 'start': Error in unlist(genomicData) : argument not a list
Could this error have something to do with the warning that Im getting:
dxd <- estimateDispersions( dxd ) using supplied model matrix using supplied model matrix Warning message: In estimateDispersionsFit(object, fitType = fitType, quiet = quiet) : the parametric fit of dispersion estimates over the mean of counts failed, which occurs when the trend is not well captured by the function y = a/x + b. A local regression fit is automatically performed, and the analysis can continue. You can specify fitType='local' or 'mean' to avoid this message if re-running the same data. When using local regression fit, the user should examine plotDispEsts(dds) to make sure the fitted line is not sharply curving up or down based on the position of individual points.
I tried plotting the dispersion (using plotDispEsts) and it doesn't look too alarming so the error sounds unrelated to me. (let me know if it would be helpful to upload it)
Any help would be very much appreciated! Many thanks in advance for your reply!
Here is my code:
dxd <- DEXSeqDataSetFromHTSeq(my_samples, sampleData=sample_ids, flattenedfile=my_gft, design= ~ sample + exon + Tissue:exon ) # I am looking at DEU in different tissues (and my sample_ids have a column named Tissue instead of condition) dxd <- estimateSizeFactors( dxd ) dxd <- estimateDispersions( dxd ) plotDispEsts( dxd ) dxd <- testForDEU( dxd ) dxd <- estimateExonFoldChanges( dxd, fitExpToVar="Tissue") dxr1 <- DEXSeqResults( dxd ) plotDEXSeq(dxr1, "ENSG00000163660", displayTranscripts=T,legend=TRUE, cex.axis=1.2, cex=1.3, lwd=1)
And here is my sessionInfo():
sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  LC_CTYPE=en_GB.ISO-8859-1 LC_NUMERIC=C LC_TIME=en_GB.ISO-8859-1 LC_COLLATE=en_GB.ISO-8859-1  LC_MONETARY=en_GB.ISO-8859-1 LC_MESSAGES=en_GB.ISO-8859-1 LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  DEXSeq_1.10.6 BiocParallel_0.4.1 DESeq2_1.4.5 RcppArmadillo_0.4.450.1.0 Rcpp_0.11.3  GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached):  annotate_1.40.1 AnnotationDbi_1.24.0 BatchJobs_1.4 BBmisc_1.7 biomaRt_2.18.0 Biostrings_2.30.1  bitops_1.0-6 brew_1.0-6 checkmate_1.4 codetools_0.2-9 DBI_0.3.1 digest_0.6.4  fail_1.2 foreach_1.4.2 genefilter_1.44.0 geneplotter_1.40.0 grid_3.0.1 hwriter_1.3.2  iterators_1.0.7 lattice_0.20-29 locfit_1.5-9.1 RColorBrewer_1.0-5 RCurl_1.95-4.3 Rsamtools_1.14.3  RSQLite_0.11.4 sendmailR_1.2-1 splines_3.0.1 statmod_1.4.20 stats4_3.0.1 stringr_0.6.2  survival_2.37-7 tools_3.0.1 XML_3.98-1.1 xtable_1.7-4 zlibbioc_1.8.0