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Old 07-11-2014, 01:41 PM   #1
Junior Member
Location: Florida

Join Date: Jul 2014
Posts: 2
Default DESeq2: minReplicatesForReplace argument

I analyze RNA-Seq data with DESeq2 package and am trying to change the argument 'minReplicatesForReplace'. However, I always get an error message about unused arguments:
> ddsHTSeq<- DESeq(ddsHTSeq, minReplicatesForReplace = 5)
Error in DESeq(ddsHTSeq, minReplicatesForReplace = 5) : 
  unused argument (minReplicatesForReplace = 5)
I read another thread here about the cooksCutoff argument that it was moved from DESeq() to results(). So I thought that perhaps it's also true for minReplicatesForReplace and tried it but again the same error:
res <- results(ddsHTSeq, minReplicatesForReplace = 5)
Error in results(ddsHTSeq, minReplicatesForReplace = 5) : 
  unused argument (minReplicatesForReplace = 5)
How can I use this argument?

P.S. sessionInfo:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] DESeq2_1.0.19             RcppArmadillo_0.4.300.8.0
[3] Rcpp_0.11.2               lattice_0.20-29          
[5] Biobase_2.20.1            GenomicRanges_1.12.5     
[7] IRanges_1.18.4            BiocGenerics_0.6.0       

loaded via a namespace (and not attached):
 [1] annotate_1.38.0      AnnotationDbi_1.22.6 DBI_0.2-7           
 [4] genefilter_1.42.0    grid_3.0.1           locfit_1.5-9.1      
 [7] RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.0.1       
[10] stats4_3.0.1         survival_2.37-7      tools_3.0.1         
[13] XML_3.98-1.1         xtable_1.7-3

Last edited by Armin_n; 07-11-2014 at 01:44 PM.
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Old 07-11-2014, 04:31 PM   #2
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Location: Montreal

Join Date: May 2013
Posts: 367

You just need to upgrade to the latest DESeq2 version.
The argument 'minReplicatesForReplace' was introduced in DESeq2 1.4.0.
You are using DESeq2 1.10.19.
The current DESeq2 version is 1.4.5.
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Old 07-12-2014, 08:12 AM   #3
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Posts: 2

Thank you, blancha!
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