Question

Error in RnaSeqGeneEdgeRQL

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Kevin • 0

@kevin-16791

Last seen 6.4 years ago

I'm learing about Bioconductor，try to work on Bioconductor>>Workflow Package>>RnaSeqGeneEdgeRQL When i run the codes

y <- DGEList(GenewiseCounts[,-1], group=group, genes=GenewiseCounts[,1,drop=FALSE])

there is error：

Error in .isAllZero(counts) : counts must be positive finite values

check ?DGEList() it shows "counts numeric matrix of read counts." I thought count shoule be matrix，so try to convert GenewiseCounts to matrix by as.matrix() The error still exists How can I fix it?

code address，the error codes at line 43 http://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.R

dgelist edger RnaSeqGeneEdgeRQL • 1.9k views

ADD COMMENT • link updated 6.4 years ago by Gordon Smyth 52k • written 6.4 years ago by Kevin • 0

score 0 · Answer 1 · 2018-08-04

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Gordon Smyth 52k

@gordon-smyth

Last seen 6 hours ago

WEHI, Melbourne, Australia

There is no error in the RnaSeqGeneEdgeRQL workflow, which runs perfectly as stated. The output from all the code can be seen here.

It appears from the error message that you may have tried to use a matrix of GenewiseCounts that contains negative or NA values. That is naturally not allowed.

Have a read of the Posting Guide. Please check that you are using the latest release of Bioconductor and please show the output from sessionInfo().

ADD COMMENT • link 6.4 years ago Gordon Smyth 52k

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Thank you for your answer

however，as you say, I just copy codes form that page and paste in Rstudio Source editor.

I didn't change any thing. and the error is still

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] RnaSeqGeneEdgeRQL_1.2.3 GO.db_3.6.0             org.Mm.eg.db_3.6.0     
 [4] AnnotationDbi_1.42.1    IRanges_2.14.10         S4Vectors_0.18.3       
 [7] Biobase_2.40.0          BiocGenerics_0.26.0     gplots_3.0.1           
[10] edgeR_3.22.3            limma_3.36.2            BiocInstaller_1.30.0   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18       bit_1.1-14         lattice_0.20-35    blob_1.1.1        
 [5] caTools_1.17.1.1   tools_3.5.1        grid_3.5.1         KernSmooth_2.23-15
 [9] DBI_1.0.0          gtools_3.8.1       bit64_0.9-7        digest_0.6.15     
[13] bitops_1.0-6       memoise_1.1.0      RSQLite_2.1.1      gdata_2.18.0      
[17] compiler_3.5.1     locfit_1.5-9.1     pkgconfig_2.0.1

ADD REPLY • link 6.4 years ago Kevin • 0

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Thank you for providing more details of your session. I am baffled what the problem might because the same code works fine for me and for others. I am running the same version of R and the same versions of all the packages as you are. The only differences are:

I'm not running R Studio.
You're using a Chinese locale for R.
You're using Windows 8 instead of Windows 10.

In principle, none of the above should make any difference. However, could you please trying running the code in plain R instead of in R Studio?

Also, could you try this code:

Counts <- as.matrix(GenewiseCounts[,-1])
summary(Counts)

What is the output?

ADD REPLY • link 6.4 years ago Gordon Smyth 52k

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Thank you for your help.

I try it on another computer in lab.

These codes run correctly

Maybe the problem is my pc

ADD REPLY • link 6.4 years ago Kevin • 0