[BioC] easyRNASeq and edgeR

[René Böttcher [guest]]

Dear all,

I am currently trying to use easyRNASeq in order to create a DGElist object for edgeR. However, when I run the function on my samples (as shown below), I encounter an error message AFTER counting:

Preparing output 
Calculating library sizes from column totals.
Normalizing counts 
Error in .local(obj, ...) : 
  You need to estimate the common dispersion before using this function.

Here's my call the easyRNASeq function:
	dgeList <- easyRNASeq(organism="Hsapiens",
	                annotationMethod="biomaRt",
	                gapped=TRUE,
			count="exons",
			filesDirectory = "/media/sf_Storage1/RNAseq",
			pattern="*_mapping\\.bam$",
			recursive=T,
	                normalize=TRUE,
			outputFormat="edgeR",
			conditions=conditions
		)

I am following the provided online manual which does not mention any dispersion estimation. Does anyone have an idea how to fix this?

Best regards,
René

 -- output of sessionInfo(): 

Output:
...
Processing G_349_mapping.bam 
Updating the read length information. 
The alignments are gapped. 
Minimum length of 1 bp. 
Maximum length of 101 bp. 
Preparing output 
Calculating library sizes from column totals.
Normalizing counts 
Error in .local(obj, ...) : 
  You need to estimate the common dispersion before using this function.
In addition: There were 33 warnings (use warnings() to see them)


> sessionInfo()
R version 2.15.2 (2012-10-26)
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  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 easyRNASeq_1.4.2                  
 [3] ShortRead_1.16.1                   latticeExtra_0.6-24               
 [5] RColorBrewer_1.0-5                 Rsamtools_1.10.1                  
 [7] DESeq_1.10.1                       lattice_0.20-10                   
 [9] locfit_1.5-8                       BSgenome_1.26.1                   
[11] GenomicRanges_1.10.3               Biostrings_2.26.2                 
[13] IRanges_1.16.3                     edgeR_3.0.2                       
[15] limma_3.14.1                       biomaRt_2.14.0                    
[17] Biobase_2.18.0                     genomeIntervals_1.14.0            
[19] BiocGenerics_0.4.0                 intervals_0.13.3                  

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.2 bitops_1.0-4.1      
 [4] DBI_0.2-5            genefilter_1.40.0    geneplotter_1.36.0  
 [7] grid_2.15.2          hwriter_1.3          RCurl_1.95-1.1      
[10] RSQLite_0.11.2       splines_2.15.2       stats4_2.15.2       
[13] survival_2.36-14     tools_2.15.2         XML_3.95-0.1        
[16] xtable_1.7-0         zlibbioc_1.4.0      


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