[BioC] Re : Filtering of data

[James W. MacDonald]

Please don't take things off-list. We like to think of the list archives 
as a useful repository of information, and taking threads off-list 
defeats that purpose.

On 7/3/2012 4:18 PM, Deeksha Malhan wrote:
> thanx but how to convert csv into expressionset format /?

Why are your data in csv format? You said that you used the affy package 
to normalize, so at some point you would have had to have an ExpressionSet.

Anyway, there is no requirement for your data to be in an ExpressionSet. 
If you look at the help page for genefilter(), you will see that you can 
pass a matrix as well.

At this point I should warn you that the amount of help you will receive 
on this list is correlated with the apparent amount of work you have 
done yourself. We are quite helpful to those that seem to really be 
stuck, less so for those who simply want someone to tell them what to do 
at each step.

Best,

Jim


>
> On Wed, Jul 4, 2012 at 1:46 AM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     Hi Deeksha,
>
>     Each Bioconductor package has at least one vignette that should
>     help you get started. For instance, genefilter has this one:
>
>     http://bioconductor.org/packages/2.10/bioc/vignettes/genefilter/inst/doc/howtogenefilter.pdf
>
>     Best,
>
>     Jim
>
>
>
>
>     On 7/3/2012 3:30 PM, Deeksha [guest] wrote:
>
>         I have done the normalization of my dataset using bioconductor
>         affy but now i am having a problem in the filtering of the
>         normalized dataset,I don't know how to do it?
>         Help me in resolving the problem
>
>
>
>           -- output of sessionInfo():
>
>         I dont know the code for it
>
>         --
>         Sent via the guest posting facility at bioconductor.org
>         <http://bioconductor.org>.
>
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>
>     -- 
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
>     4225 Roosevelt Way NE, # 100
>     Seattle WA 98105-6099
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099