I get an error message when converting a DGEList (edgeR) to DESeqDataSet (DESeq2) in DEFormats. Following is a part of the R window that reported an error. Please let me know if there is a remedy for this problem.
Thanks!
> gr=rep(c("untreated","OHT","untreated","OHT","untreated","OHT","untreated","OHT"))
> dge=DGEList( counts = counttable[, 4:11], genes = counttable[, 2], group=gr )
> dge
An object of class "DGEList"
$counts
387 387OHT 388 388OHT 436 436OHT 437 437OHT
2 3695 4374 2957 4086 5878 5786 5325 6108
3 2788 3183 2308 2864 5075 3894 4703 4578
4 5749 7431 3728 6961 8128 9878 7761 13023
5 26 32 18 38 37 42 39 41
6 8185 5028 5846 4509 7907 4566 7246 5350
22968 more rows ...
$samples
group lib.size norm.factors
387 untreated 76066299 1
387OHT OHT 63754425 1
388 untreated 55203131 1
388OHT OHT 62939421 1
436 untreated 82129140 1
436OHT OHT 65891411 1
437 untreated 72802702 1
437OHT OHT 75083124 1
$genes
[1] "Eea1" "Adgrg6" "Osbpl8" "Ttc41" "Mars"
22968 more rows ...
> library(DEFormats)
> dds = as.DESeqDataSet(dge)
Error in .find_start_end_cols(df_colnames0, start.field0, end.field0) :
cannnot determine start/end columns
Can you
- make sure you use latest versions, and
- post sessionInfo() ?
Thanks for your reply!
I get the same error in my Mac, Ubuntu, or Windows... Following is a copy of one of such sessions, including sessionInfo() output.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
> gr=rep(c("untreated","OHT"), 4)
> dge=DGEList(counts = rawcounts[, 4:11], genes = rawcounts[, 1:3], group=gr )
> ## converting the DGE object to DESeqDataSet (having a trouble at this step!)
>
> dds = as.DESeqDataSet(dge)
Error in .find_start_end_cols(df_colnames0, start.field0, end.field0) :
cannnot determine start/end columns
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)
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 utils
[7] datasets methods base
other attached packages:
[1] DEFormats_1.0.2 edgeR_3.14.0
[3] limma_3.28.19 DESeq2_1.12.4
[5] SummarizedExperiment_1.2.3 Biobase_2.32.0
[7] GenomicRanges_1.24.2 GenomeInfoDb_1.8.3
[9] IRanges_2.6.1 S4Vectors_0.10.3
[11] BiocGenerics_0.18.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.6 RColorBrewer_1.1-2 plyr_1.8.4
[4] XVector_0.12.1 tools_3.3.1 zlibbioc_1.18.0
[7] rpart_4.1-10 checkmate_1.8.1 RSQLite_1.0.0
[10] annotate_1.50.0 gtable_0.2.0 lattice_0.20-33
[13] Matrix_1.2-6 DBI_0.5 gridExtra_2.2.1
[16] genefilter_1.54.2 cluster_2.0.4 locfit_1.5-9.1
[19] grid_3.3.1 nnet_7.3-12 data.table_1.9.6
[22] AnnotationDbi_1.34.4 XML_3.98-1.4 survival_2.39-4
[25] BiocParallel_1.6.6 foreign_0.8-66 latticeExtra_0.6-28
[28] Formula_1.2-1 geneplotter_1.50.0 ggplot2_2.1.0
[31] backports_1.0.3 Hmisc_3.17-4 scales_0.4.0
[34] splines_3.3.1 colorspace_1.2-6 xtable_1.8-2
[37] acepack_1.3-3.3 munsell_0.4.3 chron_2.3-47
Dear Akira,
thank you for reporting your problems with DEFormats. The error message indicates that there might be a problem with your gene annotation. Can you please provide a sample (or a subset of)
counttablewhich you are using and which triggers the error?Cheers,
Andrzej