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Old 09-24-2012, 06:03 PM   #1
fpadilla
Francisco Padilla O.
 
Location: Columbus Ohio

Join Date: Jul 2011
Posts: 5
Default DEXSeq error in estimateDispersions: match.arg(start.method, c("log(y)", "mean"))

Hey Guys:

I got the following error many times while calling estimateDispersions:

Error in match.arg(start.method, c("log(y)", "mean")) : 'arg' must be NULL or a character vector

Below is the code I'm runing, the weird thing is execution of estimateDispersions is finished and continue to fitDispersionFunction, when it is stopped because estimateDispersions failed.

Code:
exonStats = read.HTSeqCounts(
                countfiles = file.path("./", paste(rownames(samples),"HTSeqCount.txt",sep=".") ),
		design = samples, flattenedfile = annotationFile)

exonStats <- estimateSizeFactors(exonStats)
exonStats <- estimateDispersions(exonStats, quiet=TRUE) # Error is here
exonStats <- fitDispersionFunction(exonStats) # Execution stop here
Also, I have a few datasets for testing and still I get error. Here is the experiment design

Code:
> samples
       condition replicate        type
31 4cm from base         1 single-read
32 4cm from base         2 single-read
33           tip         1 single-read
34           tip         2 single-read
This is the session info:
Code:
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-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  tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] multicore_0.1-7 DEXSeq_1.0.2    Biobase_2.14.0 

loaded via a namespace (and not attached):
[1] hwriter_1.3    plyr_1.7.1     statmod_1.4.15 stringr_0.6.1
I'll appreciate your help !

Francisco
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