[BioC] edgeR reading data

[Gordon K Smyth]

Dear Li,

Have you read the documentation page for readDGE()?  The whole purpose of 
readDGE() is to combine the files into one table for you.  It also 
computes the library sizes for you automatically.  It seems to me that the 
documentation and User's Guide tells you these things plainly enough.

If the documentation isn't enough, could you please re-read Alessandro 
Guffanti's email to you.  He has explained even more clearly how readDGE() 
reads multiple files at a time.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
smyth at wehi.edu.au
http://www.wehi.edu.au
http://www.statsci.org/smyth

On Fri, 13 Apr 2012, Wang, Li wrote:

> 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 did not 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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