[BioC] Aligned RNA-seq data to ranked list of genes

[James W. MacDonald]

That's not how you install packages. Use biocLite():

http://www.bioconductor.org/docs/install/

L. Mohammadi wrote:
> Hi All
> 
> My problem is that I need to install
> HuEx10stv2cdf R package, but I don't know how.
> I found several zip file for that, but it does not work, it has this error
> 
>> utils:::menuInstallLocal()
> Error in gzfile(file, "r") : cannot open the connection
> In addition: Warning messages:
> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
> 2: In gzfile(file, "r") :
>   cannot open compressed file 'huex10stv2cdf_1.15.0.tar.gz/DESCRIPTION',
> probable reason 'No such file or directory'
> 
> 
> the problem is that I want to do normalization for exon arrays and the
> probe names do not match with the ones from U133A for example. So, I need
> to make sure that the names are ok.
> 
> could you please help me. Thanks very much.
> 
> Best
> Leila
> 
> 
> 
>> One possibility is Genominator which uses an SQLite backend for
>> storing the data and does require a bit of time in setting up the
>> data, but you can also do a pipeline entirely in R using
>> IRanges/GenomicRanges and ShortRead.
>>
>> Kasper
>>
>> On Tue, May 25, 2010 at 11:22 AM,  <paulig2001 at yahoo.co.uk> wrote:
>>> Hello,
>>>
>>> I've got aligned rna-seq data (aligned using MAQ) for a sample and want
>>> to turn it into a list of genes ranked by their expression level in that
>>> sample. I'm wondering if anybody can point me towards a tutorial or a
>>> package that would allow me to do this?
>>>
>>> Thanks a bunch.
>>>
>>> Paul
>>>
>>>
>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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