[BioC] edgeR reading data

[Wang, Li]

Dear Gordon

Thanks very much for your reply. 
My data are now in txt format. They are separate files, each representing a sample. In each file, I specify two columns, one for gene Name, the other for expression value (total exon reads, no transformation). 
I am thinking of the readDGE function as suggested in the manual. I assume that in the function, each time only one file can be red. Then I did to do readDGE for couple of times. 
And then I donot know how to combine these reads into one table. 
Also I didnot give any information about library size. How could it be computed from the counts?

I appreciate your help  a lot!

Best wishes
Li
________________________________________
From: Gordon K Smyth [smyth at wehi.EDU.AU]
Sent: Thursday, April 12, 2012 7:06 PM
To: Wang, Li
Cc: Bioconductor mailing list
Subject: edgeR reading data

Dear Li,

It seems to me that there are four case studies in the edgeR User's Guide
that give fully worked examples of reading data into R and into edgeR.
Perhaps you might explain where you're trying to import the data from,
i.e., what format the data are in now.

In his reply, Alessandro Guffanti has explained a good way to read data
in, and there are others.

Best wishes
Gordon

> Date: Wed, 11 Apr 2012 13:42:18 -0500
> From: "Wang, Li" <li.wang at ttu.edu>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Subject: [BioC] edgeR reading data
>
> Dear List
>
> I am a very starter in edgeR analyses. When reading through the User
> Guide and homepage of edgeR, I did not find any examples of the
> importing data. My RNA-seq data can be divided into two groups, which
> then could be divided into two subgroups. And each subgroup has 8
> replicates. I am writing to ask if someone can give me a small example
> of the data that could be red in edgeR.
>
> I would appreciate your help a lot!
>
> Thanks
> Li

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