Error to convert a DGEList to DESeqDataSet in DEFormats
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@akira-imamoto-11332
Last seen 8.5 years ago
USA/Chicago/University of Chicago

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

 

 

DEFormats DESeq2 edger • 1.8k views
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Can you

- make sure you use latest versions, and

- post sessionInfo() ?

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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 

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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) counttable which you are using and which triggers the error?

Cheers,

Andrzej

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