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I tried to follow the DESeq2 tutorial, and ended up with a error.
library("pasilla")
library("DESeq2")
pasCts <- system.file("extdata", "pasilla_gene_counts.tsv", package="pasilla", mustWork=TRUE)
pasAnno <- system.file("extdata", "pasilla_sample_annotation.csv", package="pasilla", mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep="\t",row.names="gene_id"))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c("condition","type")]
rownames(coldata) <- sub("fb", "", rownames(coldata))
cts <- cts[, rownames(coldata)]
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~ condition)
featureData <- data.frame(gene=rownames(cts))
mcols(dds) <- DataFrame(mcols(dds), featureData)
dds <- DESeq(dds)
res <- results(dds)
The error is:
Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) :
the objects to concatenate must be DESeqResults objects (or NULLs)
Should I wait the new version? Is the new version different from the previous ones?
R Under development (unstable) (2018-01-08 r74099)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DESeq2_1.19.14 SummarizedExperiment_1.9.5
[3] DelayedArray_0.5.15 BiocParallel_1.13.1
[5] matrixStats_0.52.2 Biobase_2.39.1
[7] GenomicRanges_1.31.3 GenomeInfoDb_1.15.1
[9] IRanges_2.13.5 S4Vectors_0.17.17
[11] BiocGenerics_0.25.1 pasilla_1.7.0
loaded via a namespace (and not attached):
[1] genefilter_1.61.0 locfit_1.5-9.1 splines_3.5.0
[4] lattice_0.20-35 colorspace_1.3-2 htmltools_0.3.6
[7] base64enc_0.1-3 blob_1.1.0 survival_2.41-3
[10] XML_3.98-1.9 rlang_0.1.6 pillar_1.0.1
[13] DBI_0.7 foreign_0.8-70 bit64_0.9-7
[16] RColorBrewer_1.1-2 GenomeInfoDbData_1.1.0 plyr_1.8.4
[19] stringr_1.2.0 zlibbioc_1.25.0 munsell_0.4.3
[22] gtable_0.2.0 htmlwidgets_0.9 memoise_1.1.0
[25] latticeExtra_0.6-28 knitr_1.18 geneplotter_1.57.0
[28] AnnotationDbi_1.41.4 htmlTable_1.11.1 Rcpp_0.12.14
[31] acepack_1.4.1 xtable_1.8-2 scales_0.5.0
[34] backports_1.1.2 checkmate_1.8.5 Hmisc_4.1-1
[37] annotate_1.57.2 XVector_0.19.1 bit_1.1-12
[40] gridExtra_2.3 ggplot2_2.2.1 digest_0.6.13
[43] stringi_1.1.6 grid_3.5.0 tools_3.5.0
[46] bitops_1.0-6 magrittr_1.5 RSQLite_2.0
[49] lazyeval_0.2.1 RCurl_1.95-4.10 tibble_1.4.1
[52] Formula_1.2-2 cluster_2.0.6 Matrix_1.2-12
[55] data.table_1.10.4-3 rstudioapi_0.7 rpart_4.1-12
[58] nnet_7.3-12 compiler_3.5.0
BTW: thanks a lot to the DESeq2 team. You are doing a wonderful job.
I get this same error for my devel branch packages. I'll look into it today.
I haven't figured a solution but I have a minimal example. The problem comes when I try to add the padj column to res:
Where
resis a DESeqResults object, which contains DataFrame.I get the same error with this simple example:
setClass("myDataFrame", contains="DataFrame") d <- DataFrame(x=1:5) dd <- new("myDataFrame", d) d$y <- 1:5 dd$y <- 1:5 Error in concatenateObjects(x, objects, ignore.mcols = ignore.mcols) : the objects to concatenate must be myDataFrame objects (or NULLs) Calls: $<- ... c -> .local -> concatenateObjects -> concatenateObjectsWith this traceback():
> traceback() 19: stop(wmsg("the objects to concatenate must be ", class(.Object), " objects (or NULLs)")) 18: concatenateObjects(x, objects, ignore.mcols = ignore.mcols) 17: concatenateObjects(x, objects, ignore.mcols = ignore.mcols) 16: .local(x, ...) 15: c(x, value) 14: c(x, value) 13: coerce2(c(x, value), x) 12: coerce2(c(x, value), x) 11: .append_list_element(x, value, name) 10: setListElement(x, i, value) 9: setListElement(x, i, value) 8: .nextMethod(x, i, value = value) 7: eval(call, callEnv) 6: eval(call, callEnv) 5: callNextMethod(x, i, value = value) 4: `[[<-`(`*tmp*`, name, value = 1:5) 3: `[[<-`(`*tmp*`, name, value = 1:5) 2: `$<-`(`*tmp*`, y, value = 1:5) 1: `$<-`(`*tmp*`, y, value = 1:5) > sessionInfo() R Under development (unstable) (2017-12-07 r73859) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /Users/love/bin/R/lib/libRblas.dylib LAPACK: /Users/love/bin/R/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats4 stats graphics grDevices datasets utils [8] methods base other attached packages: [1] apeglm_1.1.9 DESeq2_1.19.15 [3] airway_0.113.0 SummarizedExperiment_1.9.5 [5] DelayedArray_0.5.15 BiocParallel_1.13.1 [7] matrixStats_0.52.2 Biobase_2.39.1 [9] GenomicRanges_1.31.3 GenomeInfoDb_1.15.1 [11] IRanges_2.13.5 S4Vectors_0.17.17 [13] BiocGenerics_0.25.1 BiocInstaller_1.29.3 [15] rmarkdown_1.8 testthat_2.0.0 [17] devtools_1.13.4 loaded via a namespace (and not attached): [1] bit64_0.9-7 splines_3.5.0 Formula_1.2-2 [4] latticeExtra_0.6-28 blob_1.1.0 GenomeInfoDbData_1.1.0 [7] numDeriv_2016.8-1 pillar_1.0.1 RSQLite_2.0 [10] backports_1.1.1 lattice_0.20-35 bbmle_1.0.20 [13] digest_0.6.12 RColorBrewer_1.1-2 XVector_0.19.1 [16] checkmate_1.8.5 colorspace_1.3-2 htmltools_0.3.6 [19] Matrix_1.2-12 plyr_1.8.4 XML_3.98-1.9 [22] emdbook_1.3.9 genefilter_1.61.0 zlibbioc_1.25.0 [25] xtable_1.8-2 scales_0.5.0 htmlTable_1.11.1 [28] tibble_1.4.1 annotate_1.57.2 ggplot2_2.2.1 [31] withr_2.1.1 nnet_7.3-12 lazyeval_0.2.1 [34] survival_2.41-3 magrittr_1.5 memoise_1.1.0 [37] evaluate_0.10.1 MASS_7.3-48 xml2_1.1.1 [40] foreign_0.8-70 tools_3.5.0 data.table_1.10.4-3 [43] stringr_1.2.0 locfit_1.5-9.1 munsell_0.4.3 [46] cluster_2.0.6 AnnotationDbi_1.41.4 compiler_3.5.0 [49] rlang_0.1.6 grid_3.5.0 RCurl_1.95-4.8 [52] rstudioapi_0.7 htmlwidgets_0.9 bitops_1.0-6 [55] base64enc_0.1-3 gtable_0.2.0 roxygen2_6.0.1 [58] DBI_0.7 R6_2.2.2 gridExtra_2.3 [61] knitr_1.17 bit_1.1-12 commonmark_1.4 [64] Hmisc_4.0-3 rprojroot_1.2 stringi_1.1.6 [67] Rcpp_0.12.14 geneplotter_1.57.0 rpart_4.1-12 [70] acepack_1.4.1 coda_0.19-1I started a new thread here to see if S4Vectors authors can help
Adding a column to a class that contains DataFrame
Thanks a lot!
I will wait for their fix.
(BTW: BioConductor recommends that
seq_len()orseq_along()be used instead of1:...:-)