DESeq2: minReplicatesForReplace argument

[Armin_n]

Hi,
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)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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

[blancha]

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.

[Armin_n]

Thank you, blancha!