Hi,
I am trying to export the html file for the DEXSeq results, but keep getting a warning message, when running DEXSeqHTML.
here is the script I am running:
CR4W0h.CTRL0hdxd <- DEXSeqDataSetFromHTSeq(CR4W0h.CTRL0hfiles, sampleData = CR4W0h.CTRL0hsampleTable, design = ~sample + exon + treatment:exon, flattenedfile = flattenedFile) CR4W0h.CTRL0hdxd <- CR4W0h.CTRL0hdxd[1:1000,] # subsetting the data CR4W0h.CTRL0hdxd <- estimateDispersions(CR4W0h.CTRL0hdxd, BPPARAM = BPPARAM) CR4W0h.CTRL0hdxd = testForDEU( CR4W0h.CTRL0hdxd, BPPARAM = BPPARAM)CR4W0h.CTRL0hdxd = estimateExonFoldChanges( CR4W0h.CTRL0hdxd, fitExpToVar="treatment", BPPARAM = BPPARAM) CR4W0h.CTRL0hdxr = DEXSeqResults( CR4W0h.CTRL0hdxd ) #export the counts for each exon in a table: ## read counts dir.create("A1.CR4W0h.CTRL0h") genemap <- getBM( attributes = c("ensembl_gene_id", "entrezgene", "mgi_id", "mgi_symbol", "external_gene_name"), filters = "ensembl_gene_id", values = as.character(unique(CR4W0h.CTRL0hdxr$groupID)), mart = ensembl ) row.names(genemap) <- genemap[,1] ## export the html for the sig. deregulated exons/genes DEXSeqHTML(CR4W0h.CTRL0hdxr , FDR=.99, color=c("#00CC00", "#FF0000"),file = "A1.CR4W0h.CTRL0h.html", path = "A1.CR4W0h.CTRL0h", extraCols= genemap, BPPARAM = BPPARAM)
Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
I get the html file and the folder with the images, but there are no plots there.
(The FDR is set to 0.9, because I am using a subset of my data (first 1000 genes in the dxd object) to speed up the testing.)
Is there any reason, why I don't get the plots of normalized counts?
thanks
Assa
Below is some info about the dxr object:
> names(CR4W0h.CTRL0hdxr) [1] "groupID" "featureID" "exonBaseMean" [4] "dispersion" "stat" "pvalue" [7] "padj" "CR4Wo" "ctrl" [10] "log2fold_ctrl_CR4Wo" "genomicData" "countData" [13] "transcripts > head(CR4W0h.CTRL0hdxr) LRT p-value: full vs reduced DataFrame with 6 rows and 13 columns groupID featureID exonBaseMean dispersion <character> <character> <numeric> <numeric> ENSMUSG00000000001:E001 ENSMUSG00000000001 E001 55.190150 0.006387267 ENSMUSG00000000001:E002 ENSMUSG00000000001 E002 9.096948 0.006822635 ENSMUSG00000000001:E003 ENSMUSG00000000001 E003 7.069048 0.010276909 ENSMUSG00000000001:E004 ENSMUSG00000000001 E004 10.239692 0.005841850 ENSMUSG00000000001:E005 ENSMUSG00000000001 E005 6.997248 0.008234490 ENSMUSG00000000001:E006 ENSMUSG00000000001 E006 9.971844 0.014578142 stat pvalue padj CR4Wo ctrl <numeric> <numeric> <numeric> <numeric> <numeric> ENSMUSG00000000001:E001 1.94426740 0.16320593 0.9866054 13.254746 14.010069 ENSMUSG00000000001:E002 0.03265748 0.85659221 0.9911929 5.889862 5.807485 ENSMUSG00000000001:E003 0.12982024 0.71861849 0.9911929 5.278806 5.063725 ENSMUSG00000000001:E004 0.13516393 0.71313686 0.9911929 6.242174 6.037368 ENSMUSG00000000001:E005 3.15406029 0.07573829 0.9866054 5.668869 4.499273 ENSMUSG00000000001:E006 0.43437184 0.50985151 0.9911929 5.818799 6.325129 log2fold_ctrl_CR4Wo genomicData <numeric> <GRanges> ENSMUSG00000000001:E001 0.07995509 3:-:[108107280, 108109316] ENSMUSG00000000001:E002 -0.02032015 3:-:[108109403, 108109612] ENSMUSG00000000001:E003 -0.06001257 3:-:[108111935, 108112088] ENSMUSG00000000001:E004 -0.04812888 3:-:[108112473, 108112602] ENSMUSG00000000001:E005 -0.33336897 3:-:[108115763, 108115891] ENSMUSG00000000001:E006 0.12037342 3:-:[108118301, 108118458] countData transcripts <integer> <list> ENSMUSG00000000001:E001 53 ######## ENSMUSG00000000001:E002 14 ######## ENSMUSG00000000001:E003 11 ######## ENSMUSG00000000001:E004 10 ######## ENSMUSG00000000001:E005 14 ######## ENSMUSG00000000001:E006 15 ########
> sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS 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=en_US.UTF-8 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] DEXSeq_1.16.2 DESeq2_1.10.0 [3] RcppArmadillo_0.6.200.2.0 Rcpp_0.12.2 [5] SummarizedExperiment_1.0.1 GenomicRanges_1.22.1 [7] GenomeInfoDb_1.6.1 IRanges_2.4.4 [9] S4Vectors_0.8.3 Biobase_2.30.0 [11] BiocGenerics_0.16.1 BiocParallel_1.4.0 loaded via a namespace (and not attached): [1] genefilter_1.52.0 statmod_1.4.22 locfit_1.5-9.1 [4] reshape2_1.4.1 splines_3.2.2 lattice_0.20-33 [7] colorspace_1.2-6 survival_2.38-3 XML_3.98-1.3 [10] foreign_0.8-66 DBI_0.3.1 RColorBrewer_1.1-2 [13] lambda.r_1.1.7 plyr_1.8.3 stringr_1.0.0 [16] zlibbioc_1.16.0 Biostrings_2.38.2 munsell_0.4.2 [19] gtable_0.1.2 futile.logger_1.4.1 hwriter_1.3.2 [22] latticeExtra_0.6-26 geneplotter_1.48.0 biomaRt_2.26.0 [25] AnnotationDbi_1.32.0 proto_0.3-10 acepack_1.3-3.3 [28] xtable_1.8-0 scales_0.3.0 Hmisc_3.17-0 [31] annotate_1.48.0 XVector_0.10.0 Rsamtools_1.22.0 [34] gridExtra_2.0.0 ggplot2_1.0.1 digest_0.6.8 [37] stringi_1.0-1 grid_3.2.2 tools_3.2.2 [40] bitops_1.0-6 magrittr_1.5 RCurl_1.95-4.7 [43] RSQLite_1.0.0 Formula_1.2-1 cluster_2.0.3 [46] futile.options_1.0.0 MASS_7.3-45 rpart_4.1-10 [49] nnet_7.3-11