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Old 07-11-2014, 02:41 PM   #1
Armin_n
Junior Member
 
Location: Florida

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

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:
Code:
> 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:
Code:
res <- results(ddsHTSeq, minReplicatesForReplace = 5)
Error in results(ddsHTSeq, minReplicatesForReplace = 5) : 
  unused argument (minReplicatesForReplace = 5)
How can I use this argument?


P.S. sessionInfo:
Code:
> 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

Last edited by Armin_n; 07-11-2014 at 02:44 PM.
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Old 07-11-2014, 05:31 PM   #2
blancha
Senior Member
 
Location: Montreal

Join Date: May 2013
Posts: 367
Default

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, 09:12 AM   #3
Armin_n
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Location: Florida

Join Date: Jul 2014
Posts: 2
Default

Thank you, blancha!
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