I am trying to analyze my smallRNAseq data with Deseq2 and to run ReportingTools on it.
I have different treatments and timepoints, I saw that you have a coef option to tell where to do the comparison with, but my data set then will exclude another timepoint or treatment. I am wondering if it is possible to get all pairwise comparisons from the data set as log2FC, or to input the results from Deseq2 into those columns and keep the barplots.
I tried to do them first as pairwise comparisons, but that did not seem to work properly:
dds.sub1 <- dds[ , dds$condition %in% c("M_3h", "R_3h") ]
dds.sub1$condition <- droplevels(dds.sub1$condition)
dds.sub1$type <- droplevels(dds.sub1$type)
publish(dds.sub1,des2Report, pvalueCutoff=1.1, annotation.db="org.Hs.egENSEMBL", factor = colData(dds.sub1)$condition, reportDir=out, n = length(row.names(dds.sub1)))
Error in counts(object) %*% whichSamples : non-conformable arguments
In case you have a comment or suggestion on that it would be nice.
I am also wondering if there is a way to print everything, even if the calculated pvalue is NA, I have one replicate that I would not exclude, but caused that some interesting genes get a pvalue of NA, and for me would be interesting to check them.
R version 3.2.4 (2016-03-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8  LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  ReportingTools_2.10.0 knitr_1.12.3 pheatmap_1.0.8 stringr_1.0.0 RColorBrewer_1.1-2  gplots_3.0.1 DESeq2_1.10.1 RcppArmadillo_0.6.600.4.0 Rcpp_0.12.4 SummarizedExperiment_1.0.2  GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 ggplot2_2.1.0 geneplotter_1.48.0 annotate_1.48.0  XML_3.98-1.4 lattice_0.20-33 genefilter_1.52.1 org.Hs.eg.db_3.2.3 AnnotationDbi_1.32.3  IRanges_2.4.8 S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1 scatterplot3d_0.3-37  RSQLite_1.0.0 DBI_0.3.1 loaded via a namespace (and not attached):  edgeR_3.12.1 splines_3.2.4 R.utils_2.3.0 gtools_3.5.0 Formula_1.2-1  latticeExtra_0.6-28 RBGL_1.46.0 BSgenome_1.38.0 Rsamtools_1.22.0 Category_2.36.0  biovizBase_1.18.0 limma_3.26.9 XVector_0.10.0 colorspace_1.2-6 ggbio_1.18.5  R.oo_1.20.0 Matrix_1.2-5 plyr_1.8.3 OrganismDbi_1.12.1 GSEABase_1.32.0  biomaRt_2.26.1 zlibbioc_1.16.0 xtable_1.8-2 GO.db_3.2.2 scales_0.4.0  gdata_2.17.0 BiocParallel_1.4.3 PFAM.db_3.2.2 GenomicFeatures_1.22.13 nnet_7.3-12  survival_2.39-2 magrittr_1.5 R.methodsS3_1.7.1 GGally_1.0.1 hwriter_1.3.2  foreign_0.8-66 GOstats_2.36.0 graph_1.48.0 BiocInstaller_1.20.3 tools_3.2.4  munsell_0.4.3 locfit_1.5-9.1 cluster_2.0.4 lambda.r_1.1.7 Biostrings_2.38.4  caTools_1.17.1 futile.logger_1.4.1 grid_3.2.4 RCurl_1.95-4.8 dichromat_2.0-0  VariantAnnotation_1.16.4 AnnotationForge_1.12.2 bitops_1.0-6 gtable_0.2.0 reshape_0.8.5  reshape2_1.4.1 GenomicAlignments_1.6.3 gridExtra_2.2.1 rtracklayer_1.30.4 Hmisc_3.17-3  futile.options_1.0.0 KernSmooth_2.23-15 stringi_1.0-1 rpart_4.1-10 acepack_1.3-3.3