Question: what does "Error: is(cds, "CountDataSet") is not TRUE" mean?
gravatar for Parham
5.6 years ago by
Parham1.5k wrote:


I am practicing DESeq2 manual (Differential analysi s of count data – the DESeq2 package). When I do varianceStabilizingTransformation with dds created from my data I get "Error: is(cds, "CountDataSet") is not TRUE". Surprisingly when I practiced the example from R's help page "Apply a variance stabilizing transformation (VST) to the count data", I got the same error again. Any suggestions? Please speak at non-bioinformatician level! 

> dds <- makeExampleDESeqDataSet(m=6)
> vsd <- varianceStabilizingTransformation(dds)
Error: is(cds, "CountDataSet") is not TRUE
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Parham1.5k

What version are you using that it's still looking for a CountDataSet? In other words, please post the output of sessionInfo(). My guess is that you just have an old version of DESeq2 that had a bug (probably from around the time that the transition was made to a DESeqDataSet object).

ADD REPLYlink written 5.6 years ago by Devon Ryan95k

However when I wanted to load the data again, at one point (section 1.2.3) I had to load DESeq again. Do you know if it is a bug or something in the scripts? Or I have to load DESeq and then detach it again to not get the above error?

> data("pasillaGenes")
Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’
Loading required package: DESeq
Error in .requirePackage(package) : 
  unable to find required package ‘DESeq’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘DESeq’
ADD REPLYlink written 5.6 years ago by Parham1.5k

Hmmm, I recall mentioning that to Simon Anders and Alejandro Reyes months ago in an email. This is/was a bug in the pasilla package. Do you have the most recent version?

ADD REPLYlink written 5.6 years ago by Devon Ryan95k

I am using R studio and it says all packaged are updated when I click update button. However here is the sessionInfo() output: 

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] pasilla_0.5.1

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         annotate_1.44.0         AnnotationDbi_1.28.1    base64enc_0.1-2         BatchJobs_1.5          
 [6] BBmisc_1.8              Biobase_2.26.0          BiocGenerics_0.12.1     BiocParallel_1.0.0      brew_1.0-6             
[11] checkmate_1.5.0         cluster_1.15.3          codetools_0.2-9         colorspace_1.2-4        DBI_0.3.1              
[16] DESeq_1.18.0            DESeq2_1.6.2            digest_0.6.4            fail_1.2                foreach_1.4.2          
[21] foreign_0.8-61          Formula_1.1-2           genefilter_1.48.1       geneplotter_1.44.0      GenomeInfoDb_1.2.3     
[26] GenomicRanges_1.18.3    ggplot2_1.0.0           grid_3.1.2              gtable_0.1.2            Hmisc_3.14-5           
[31] IRanges_2.0.0           iterators_1.0.7         lattice_0.20-29         latticeExtra_0.6-26     locfit_1.5-9.1         
[36] MASS_7.3-35             munsell_0.4.2           nnet_7.3-8              parallel_3.1.2          plyr_1.8.1             
[41] proto_0.3-10            RColorBrewer_1.0-5      Rcpp_0.11.3             RcppArmadillo_0.4.500.0 reshape2_1.4           
[46] rpart_4.1-8             RSQLite_1.0.0           S4Vectors_0.4.0         scales_0.2.4            sendmailR_1.2-1        
[51] splines_3.1.2           stats4_3.1.2            stringr_0.6.2           survival_2.37-7         tools_3.1.2            
[56] XML_3.98-1.1            xtable_1.7-4            XVector_0.6.0          
ADD REPLYlink written 5.6 years ago by Parham1.5k

I guess Alejandro never changed that. That's somewhat annoying. If you load pasilla first and Deseq2 second then perhaps that'll work.

ADD REPLYlink written 5.6 years ago by Devon Ryan95k
gravatar for Parham
5.6 years ago by
Parham1.5k wrote:

I had both DESeq and DESeq2 loaded in R. I detached DESeq and it was fine then. Thanks Devon!

ADD COMMENTlink written 5.6 years ago by Parham1.5k
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