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

[L. Mohammadi]

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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