[Bioc-sig-seq] About PhredQuality

[Martin Morgan]

On 09/07/2011 01:10 PM, wang peter wrote:
> qual<- PhredQuality(quality(quality(reads)));#1
> qual<- FastqQuality(quality(quality(reads)));#2
> readM<- as(qual, "matrix");
> pdf(file="boxplot.pdf",width=25, height = 75); # Save box plot as
> boxplot.pdf in current folder
> boxplot(as.data.frame((readM)), outline = FALSE, main="Per Cycle Read
> Quality", xlab="Cycle", ylab="Phred Quality");
>      # build per cycle boxplot
> dev.off()
>
> i wrote such coding,because PhredQuality and FastqQuality have the same
> information
> those coding can run well on windows
> but the #1 cannot run well on linux and gave such error
>
>
>> qual<- PhredQuality(quality(quality(reads)));
>> readM<- as(qual, "matrix");
> Error in as.vector(data) :
>    no method for coercing this S4 class to a vector

generally, functionality is the same across platforms when the same 
version of R (and therefore Bioconductor) is in use.

What does

   sessionInfo()

say on each machine? If the same version of R, then perhaps packages on 
one or the other machine are out of date.

   http://bioconductor.org/install/#update-bioconductor-packages

Martin

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