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one or the other machine are out of date.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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