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Old 11-20-2013, 09:35 AM   #1
JonB
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Default DESeq2 error: varianceStabilizingTransformation error

Hi,

I am simply following the DESeq2 tutorial, but I get an error during the varianceStabilizingTransformation:

Code:
> vsd <- varianceStabilizingTransformation(dds, blind=TRUE)
Error in varianceStabilizingTransformation(dds, blind = TRUE) : 
  unused argument (blind = TRUE)
>
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Old 11-21-2013, 12:57 AM   #2
dpryan
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What's the output of:
Code:
sessionInfo()
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Old 11-21-2013, 01:48 AM   #3
JonB
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Code:
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C

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

other attached packages:
 [1] pasilla_0.2.18          DESeq_1.14.0            lattice_0.20-24         locfit_1.5-9.1          DEXSeq_1.8.0           
 [6] Biobase_2.22.0          parathyroidSE_1.0.4     DESeq2_1.2.5            RcppArmadillo_0.3.920.1 Rcpp_0.10.6            
[11] BiocInstaller_1.12.0    cummeRbund_2.4.0        Gviz_1.6.0              rtracklayer_1.22.0      GenomicRanges_1.14.3   
[16] XVector_0.2.0           IRanges_1.20.5          fastcluster_1.1.11      reshape2_1.2.2          ggplot2_0.9.3.1        
[21] RSQLite_0.11.4          DBI_0.2-7               BiocGenerics_0.8.0     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.24.0   BSgenome_1.30.0        Biostrings_2.30.1      GenomicFeatures_1.14.2 Hmisc_3.12-2          
 [6] MASS_7.3-29            RColorBrewer_1.0-5     RCurl_1.95-4.1         Rsamtools_1.14.1       XML_3.95-0.2          
[11] annotate_1.40.0        biomaRt_2.18.0         biovizBase_1.10.3      bitops_1.0-6           cluster_1.14.4        
[16] colorspace_1.2-4       dichromat_2.0-0        digest_0.6.3           genefilter_1.44.0      geneplotter_1.40.0    
[21] gtable_0.1.2           hwriter_1.3            labeling_0.2           latticeExtra_0.6-26    munsell_0.4.2         
[26] plyr_1.8               proto_0.3-10           rpart_4.1-3            scales_0.2.3           splines_3.0.2         
[31] statmod_1.4.18         stats4_3.0.2           stringr_0.6.2          survival_2.37-4        tools_3.0.2           
[36] xtable_1.7-1           zlibbioc_1.8.0
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Old 11-21-2013, 03:52 AM   #4
dpryan
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It's because you have both DESeq and DESeq2 loaded. The version of that function in DESeq has a different syntax. That's why when you loaded DESeq, you got a message like:

Code:
The following objects are masked from ‘package:DESeq2’:

    estimateSizeFactorsForMatrix, getVarianceStabilizedData, plotPCA,
    varianceStabilizingTransformation
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Old 11-21-2013, 04:29 AM   #5
JonB
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Ok thanks!

I see that loading the Pasilla package from the DESeq2 tutorial forces DESeq to be loaded also. Do you know if there is any way to use the Pasilla dataset without loading DESeq?
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Old 11-21-2013, 04:37 AM   #6
dpryan
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Hmm, I never noticed that! You can just load pasilla first and then load DESeq2. That'll mask the DESeq functions. The pasilla library also requires and loads DEXSeq, which seems a bit silly as well.
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Old 11-21-2013, 04:45 AM   #7
dpryan
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I went ahead and shot Alejandro Reyes (the maintainer for pasilla) an email. Hopefully he can just change the pasilla package so that no one else gets bit by this.
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Old 11-22-2013, 01:15 AM   #8
areyes
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Thanks dpryan for your e-mail. After a short discussion with the authors of DESeq2, we agreed that the most convenient solution is that pasilla does not load DESeq or DEXSeq anymore. These changes are in the latest version of pasilla (0.2.19), which should be available in the next couple of days via biocLite.

In the meantime, you could load the objects from the pasilla vignette without loading the package like this:

data("pasillaGenes", package="pasilla")
data("pasillaExons", package="pasilla")

Thanks for noticing this issue!
Alejandro
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