what does "Error: is(cds, "CountDataSet") is not TRUE" mean?

Question

[Parham]

Hi,

I am practicing DESeq2 manual (Differential analysi s of count data - the DESeq2 package). When I do varianceStabilizingTransformationwith 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

[Devon Ryan]

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).

[Parham]

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Warning: namespace ‘DESeq’ is not available and has been replaced
by .GlobalEnv when processing object ‘pasillaGenes’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’

[Devon Ryan]

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?

[Parham]

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)

locale:
[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

[Devon Ryan]

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

Answer 1

[Parham]

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