[BioC] Regarding an issue with easyRNASeq - from Surjyendu Ray.

[Nicolas Delhomme]

Dear Surjyendu Ray,

It seems to be an issue with the edgeR API. I would need more information from you, can you please run in your R session:

library(easyRNASeq)
sessionInfo()

and send me the results?

Thanks,

Nico

P.S. I've Cc'ed the Bioconductor mailing list as it might help other users. If you do not know this mailing list and are doing analyses in R/Bioc, I would advise you to subscribe to it.

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Aug 16, 2012, at 5:53 AM, Surjyendu Ray wrote:

> Dear Sir,
>              I was running an experiment with two samples and three replicates for each sample. Here are the commands I used:
> 
> conditions = c( "HCV1", "HCV1", "HCV1", "HCM1", "HCM1", "HCM1" )
> names(conditions) <- c( "accepted_hits_ATCACG.sorted.bam", "accepted_hits_CGATGT.sorted.bam", "accepted_hits_TTAGGC.sorted.bam", "accepted_hits_CAGATC.sorted.bam", "accepted_hits_ACTTGA.sorted.bam", "accepted_hits_GATCAG.sorted.bam" )
> 
> and the easyRNASeq command:
> FM_HCV1_HCM1.count.table <- easyRNASeq( filesDirectory = "/panfs/storage.local/genacc/home/sr09m/Biomedicine research/New Drosophila analysis/Tophat_temp", organism = "Dmelanogaster", chr.sizes = as.list( seqlengths( Dmelanogaster )), readLength = 76L, annotationMethod = "gff", annotationFile = "/panfs/storage.local/genacc/home/sr09m/Biomedicine research/New Drosophila analysis/dmel-all-r5.46.gff", format = "bam", count = "exons", filenames = c( "accepted_hits_ATCACG.sorted.bam", "accepted_hits_CGATGT.sorted.bam", "accepted_hits_TTAGGC.sorted.bam", "accepted_hits_CAGATC.sorted.bam", "accepted_hits_ACTTGA.sorted.bam", "accepted_hits_GATCAG.sorted.bam" ), normalize = TRUE, outputFormat = "edgeR", conditions = conditions )
> 
> However, I got an error: 
> Error in match.arg(trend, c("none", "movingave", "tricube")) : 
>   'arg' must be NULL or a character vector
> 
> The entire log of outputs is:
> Checking arguments... 
> Fetching annotations... 
> Read 12568191 records
> Summarizing counts... 
> Processing accepted_hits_ATCACG.sorted.bam 
> Processing accepted_hits_CGATGT.sorted.bam 
> Processing accepted_hits_TTAGGC.sorted.bam 
> Processing accepted_hits_CAGATC.sorted.bam 
> Processing accepted_hits_ACTTGA.sorted.bam 
> Processing accepted_hits_GATCAG.sorted.bam 
> Preparing output 
> Calculating library sizes from column totals.
> Normalizing counts 
> Error in match.arg(trend, c("none", "movingave", "tricube")) : 
>   'arg' must be NULL or a character vector
> 
>                Please advise as to what may be going wrong.
>           Thanking you,
>                                      Yours faithfully,
>                                      Surjyendu Ray.