Question: Error to convert a DGEList to DESeqDataSet in DEFormats
0
gravatar for Akira Imamoto
3.1 years ago by
USA/Chicago/University of Chicago
Akira Imamoto0 wrote:

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

 

 

edger deseq2 deformats • 543 views
ADD COMMENTlink written 3.1 years ago by Akira Imamoto0

Can you

- make sure you use latest versions, and

- post sessionInfo() ?

ADD REPLYlink written 3.1 years ago by Wolfgang Huber13k

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 

ADD REPLYlink written 3.1 years ago by Akira Imamoto0

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

ADD REPLYlink written 3.0 years ago by Andrzej Oleś720
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