Dear Bioconductors,

I have an issue with calculating normalisation factors in edgeR. This has always i.e. on three other datasets worked just fine, which leads me baffled here.

To summarise-
-NaNs occur independently of the calcNormFactors method
-the counts appear ok
-no NaNs are present in the counts


virusDGE = calcNormFactors(virusDGE, method="TMM")
virusDGE = calcNormFactors(virusDGE, method="RLE")
virusDGE = calcNormFactors(virusDGE, method="upperquartile")


> virusDGE
An object of class "DGEList"
$samples
                      group lib.size norm.factors
counts1   	all       17          NaN
counts2   	all        8          NaN
counts3    	all       14          NaN
counts4    	all        4          NaN
counts5   	all    18218          NaN
counts6   	all    37146          NaN
counts7    	all     2579          NaN
counts8    	all     1027          NaN

$counts
            		counts1	 counts2 counts3
MuHV1_gp001                     0                     0                    0
MuHV1_gp002                     0                     0                    0
MuHV1_gp003                     0                     0                    0
MuHV1_gp004                     0                     0                    0
MuHV1_gp005                     0                     0                    0
            		counts4	 		counts5 		counts6
MuHV1_gp001                    0                     0                     1
MuHV1_gp002                    0                     4                     5
MuHV1_gp003                    0                    13                    18
MuHV1_gp004                    0                    11                     2
MuHV1_gp005                    0                     4                     6
            		counts7 		counts8
MuHV1_gp001                    0                    0
MuHV1_gp002                    0                    0
MuHV1_gp003                    3                    0
MuHV1_gp004                    3                    0
MuHV1_gp005                    2                    0



is.integer(virusDGE$counts)
#TRUE
is.na(virusDGE$counts)
#(all are FALSE)
> sum(is.na(virusDGE$counts))
#[1] 0


> 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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_2.4.6           limma_3.10.3          GenomicFeatures_1.6.9
[4] AnnotationDbi_1.16.19 Biobase_2.14.0        GenomicRanges_1.6.7  
[7] IRanges_1.12.6       

loaded via a namespace (and not attached):
 [1] biomaRt_2.10.0     Biostrings_2.22.0  BSgenome_1.22.0    DBI_0.2-5         
 [5] RCurl_1.91-1       RSQLite_0.11.1     rtracklayer_1.14.4 tools_2.14.1      
 [9] XML_3.9-4          zlibbioc_1.0.1    



I am using a custom built annotation, i.e.
virustxdb=makeTranscriptDb(transcripts, splicings, genes, chrominfo)
It seems to have worked fine so far and counted reads per feature reliably, but could this be the problem ?


Thanks for your time,

Colin Davenport


Dr. Colin Davenport
Bioinformatician
Tümmler Group
PFZ S0-7440
Hannover Medical School
Germany
davenport [dot] colin <at> mh-hannover.de
0049 511532-8733

Genomics software available at
http://genomics1.mh-hannover.de

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