I have import data on deseq2 using tximport from rsem results.
After create the rlog object I try to use mroast and camera on some pathway. This is the script I use:
files <- list.files(path=path, pattern="*.ensembl.csv", full.names=T, recursive=FALSE) tipo<-list() result_camera<-data.frame("Ngenes"=numeric(),"Direction"=character(),"PValue"=numeric(),"name"=character(),stringsAsFactors = F) result_mroast<-data.frame("NGenes" =numeric(),"PropDown"=numeric(),"PropUp"=numeric(),"Direction"=character(),"PValue"=numeric(), "FDR"=numeric(),"PValue.Mixed"=numeric(), "FDR.Mixed" =numeric(),stringsAsFactors = F) for(i in 1:length(files)){ ao<-strsplit(files[i],"/")[[1]] name<-ao[9] listaGeni<- read.table(files[i],header=F,sep="\t") id=ids2indices(listaGeni$V1,rownames(v)) condition<-factor(metadata$CONDITION) design<-model.matrix(formula(~ condition)) gst.camera<-camera(v,id,design = design) pi<-mroast(v,index=id,design,nrot = 99) result_mroast<-rbind(result_mroast,data.frame(pi)) result_camera<-rbind(result_camera,data.frame(gst.camera$NGenes,gst.camera$Direction,gst.camera$PValue,name)) }
There is some difference For camera for istance
28 | Up | 0.0748709564 | Bcellsmemories.csv.ensembl.csv |
for the mroast:
NGenes PropDown PropUp Direction PValue FDR PValue.Mixed FDR.Mixed
Set1 28 0.00000000 0.25000000 Up 0.34 0.34 0.17 0.17
sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.2 LTS locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods [9] base other attached packages: [1] GSEABase_1.36.0 graph_1.52.0 annotate_1.52.1 [4] XML_3.98-1.9 AnnotationDbi_1.36.2 limma_3.30.13 [7] clusterProfiler_3.2.14 DOSE_3.0.10 biomaRt_2.30.0 [10] pheatmap_1.0.8 tximportData_1.2.0 tximport_1.2.0 [13] DESeq2_1.14.1 SummarizedExperiment_1.4.0 Biobase_2.34.0 [16] GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 IRanges_2.8.2 [19] S4Vectors_0.12.2 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] tidyr_0.6.3 bit64_0.9-7 splines_3.3.2 Formula_1.2-1 [5] DO.db_2.9 latticeExtra_0.6-28 blob_1.1.0 RSQLite_2.0 [9] backports_1.1.0 lattice_0.20-35 digest_0.6.12 RColorBrewer_1.1-2 [13] XVector_0.14.1 checkmate_1.8.2 qvalue_2.6.0 colorspace_1.3-2 [17] htmltools_0.3.6 Matrix_1.2-10 plyr_1.8.4 pkgconfig_2.0.1 [21] genefilter_1.56.0 zlibbioc_1.20.0 xtable_1.8-2 GO.db_3.4.0 [25] scales_0.4.1 BiocParallel_1.8.2 htmlTable_1.9 tibble_1.3.3 [29] ggplot2_2.2.1 nnet_7.3-12 lazyeval_0.2.0 survival_2.41-3 [33] magrittr_1.5 memoise_1.1.0 foreign_0.8-69 tools_3.3.2 [37] data.table_1.10.4 stringr_1.2.0 munsell_0.4.3 locfit_1.5-9.1 [41] cluster_2.0.6 rlang_0.1.1 grid_3.3.2 RCurl_1.95-4.8 [45] htmlwidgets_0.8 igraph_1.0.1 bitops_1.0-6 base64enc_0.1-3 [49] gtable_0.2.0 DBI_0.7 reshape2_1.4.2 gridExtra_2.2.1 [53] knitr_1.16 bit_1.1-12 fastmatch_1.1-0 Hmisc_4.0-3 [57] fgsea_1.0.2 stringi_1.1.5 GOSemSim_2.0.4 Rcpp_0.12.11 [61] geneplotter_1.52.0 rpart_4.1-11 acepack_1.4.1
Note that you can get the estimated gene counts straight from the tximport list: txi$counts, you don't need DESeq2 here.
so if I use tximport$counts I obtain total different results...(if mroast see up as direction then I found down)
I don't see what the problem is. Why would you expect roast() and camera() to give the same results? They're different tests, so naturally they will give different results. In this case, neither test gives a statistically significant result, so they pretty much agree.
As I say, what's the problem?
I have this problem. Camera seem gave one results the mroast gave me a little different results. You say this is normal. So the problem is what is the right method to choose when you question is to say if there is some enrichment in this list of data? with mroast don't have any significant change with camera yes
http://imgur.com/a/6dNqA
thanks for patience help