Hi,
I am new to R and try to analyze a RNA-seq experiment using DESeq2. I've got a pretty simple RNAseq experiment (3 conditions, 2 biological replicates) but I'm having trouble getting the count data into DESeq2.
I used several ways to import my data, however always get the same error:
Error in if/while (condition) {: missing Value where TRUE/FALSE needed
Could anybody explain what is wrong?
Thank you in advance!
Johannes
countData <- as.matrix(read.table ("Seq_unnorm_null.txt", header = TRUE, sep = "\t", row.names = 1))
colData = read.table ("Seq_r_cond.txt", header = TRUE, sep = "\t", row.names = 1)
colData [["condition"]] = factor(colData[["condition"]], levels = c("inflamm", "Treg", "none"))
head(countData)
BM12_1 BM12_2 Treg_1 Treg_2 Con_1 Con_2
1700086P04Rik 0 0 1.43484e+11 0 0 0
3300005D01Rik 0 0 1.43484e+11 0 0 0
4933430I17Rik 0 0 1.43484e+11 0 0 0
5730507C01Rik 0 0 1.43484e+11 0 0 0
9330159M07Rik 0 0 1.43484e+11 0 0 0
Ak9 0 0 1.43484e+11 0 0 0
head(colData)
condition
BM12_1 inflamm
BM12_2 inflamm
Treg_1 Treg
Treg_2 Treg
Con_1 none
Con_2 none
all(rownames(colData) %in% colnames(countData))
[1] TRUE
countData <- countData[, rownames(colData)]
all(rownames(colData) == colnames(countData))
[1] TRUE
library ("DESeq2")
Lade nötiges Paket: S4Vectors
Lade nötiges Paket: stats4
Lade nötiges Paket: BiocGenerics
Lade nötiges Paket: parallel
Attache Paket: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB,
parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min
Attache Paket: ‘S4Vectors’
The following objects are masked from ‘package:base’:
colMeans, colSums, expand.grid, rowMeans, rowSums
Lade nötiges Paket: IRanges
Lade nötiges Paket: GenomicRanges
Lade nötiges Paket: GenomeInfoDb
Lade nötiges Paket: SummarizedExperiment
Lade nötiges Paket: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for
packages 'citation("pkgname")'.
dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ condition)
converting counts to integer mode
Fehler in if (all(assay(se) == 0)) { :
Fehlender Wert, wo TRUE/FALSE nötig ist
Zusätzlich: Warnmeldung:
In `mode<-`(`*tmp*`, value = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, :
NAs introduced by coercion to integer range
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 10586)
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.14.1 SummarizedExperiment_1.4.0 Biobase_2.34.0 GenomicRanges_1.26.1 GenomeInfoDb_1.10.1
[6] IRanges_2.8.1 S4Vectors_0.12.1 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.8 RColorBrewer_1.1-2 plyr_1.8.4 XVector_0.14.0 bitops_1.0-6 tools_3.3.2 zlibbioc_1.20.0
[8] digest_0.6.10 rpart_4.1-10 base64_2.0 memoise_1.0.0 RSQLite_1.1-1 annotate_1.52.0 tibble_1.2
[15] gtable_0.2.0 htmlTable_1.7 lattice_0.20-34 Matrix_1.2-7.1 DBI_0.5-1 gridExtra_2.2.1 genefilter_1.56.0
[22] stringr_1.1.0 cluster_2.0.5 knitr_1.15.1 locfit_1.5-9.1 grid_3.3.2 nnet_7.3-12 data.table_1.10.0
[29] AnnotationDbi_1.36.0 XML_3.98-1.5 survival_2.40-1 BiocParallel_1.8.1 foreign_0.8-67 latticeExtra_0.6-28 Formula_1.2-1
[36] geneplotter_1.52.0 ggplot2_2.2.0 magrittr_1.5 htmltools_0.3.5 Hmisc_4.0-1 scales_0.4.1 splines_3.3.2
[43] assertthat_0.1 xtable_1.8-2 colorspace_1.3-2 stringi_1.1.2 acepack_1.4.1 RCurl_1.95-4.8 lazyeval_0.2.0
[50] openssl_0.9.5 munsell_0.4.3
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