Question: Error in RnaSeqGeneEdgeRQL
0
gravatar for Kevin
12 months ago by
Kevin0
Kevin0 wrote:

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

ADD COMMENTlink modified 12 months ago by Gordon Smyth38k • written 12 months ago by Kevin0
Answer: Error in RnaSeqGeneEdgeRQL
0
gravatar for Gordon Smyth
12 months ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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 COMMENTlink modified 12 months ago • written 12 months ago by Gordon Smyth38k

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 REPLYlink modified 12 months ago • written 12 months ago by Kevin0

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:

  1. I'm not running R Studio.
  2. You're using a Chinese locale for R.
  3. 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 REPLYlink modified 12 months ago • written 12 months ago by Gordon Smyth38k

Thank you for your help.

I try it on another computer in lab.

These codes run correctly

Maybe the problem is my pc

ADD REPLYlink written 12 months ago by Kevin0
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