[BioC] an error from ShortRead

[Sean Davis]

On Fri, Mar 16, 2012 at 12:59 PM, wang peter <wng.peter at gmail.com> wrote:
> it works well on
>
> qual <- SolexaQuality(quality(quality(reads)))
>
> but
> that is the error place:
>  myqual_mat <- matrix(charToRaw(as.character(unlist(qual))),nrow=length(qual),
> byrow=TRUE)

Hi, Shan.

Marcus was trying to help with his email.  Instead of your code above, try:

myqual_mat = as(qual,'matrix')

Sean


> Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
> negative length vectors are not allowed
> Calls: trimRead ... matrix -> charToRaw -> unlist -> unlist -> .Call2 -> .Call
> Execution halted
>
>
>
>>> R version 2.14.1 (2011-12-22)
>>> Platform: x86_64-redhat-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
>>>
>>> --
>>> shan gao
>>> Room 231(Dr.Fei lab)
>>> Boyce Thompson Institute
>>> Cornell University
>>> Tower Road, Ithaca, NY 14853-1801
>>> Office phone: 1-607-254-1267(day)
>>> Official email:sg839 at cornell.edu
>>> Facebook:http://www.facebook.com/profile.php?id=100001986532253
>>>
>>> _______________________________________________
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>>
>>
>
>
>
> --
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
> Tower Road, Ithaca, NY 14853-1801
> Office phone: 1-607-254-1267(day)
> Official email:sg839 at cornell.edu
> Facebook:http://www.facebook.com/profile.php?id=100001986532253
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor