[BioC] readDGE

[James W. MacDonald]

Yes. And if you don't like the warning, just change groups to group.

Jim



On 6/12/2014 3:55 PM, Chinh Hoan wrote:
> Thanks Jim,
> This means that I still can process the data as usual? silly me. Again I highly appreciate your response.
> Chinh
> ________________________________________
> From: James W. MacDonald [jmacdon at uw.edu]
> Sent: Thursday, June 12, 2014 2:49 PM
> To: Chinh Hoan; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] readDGE
>
> Hi Chinh Hoan,
>
> On 6/12/2014 11:36 AM, Chinh Hoan wrote:
>> Hello all,
>> Below is my problem with readDGE. Could you please tell what should I do to fix the problem? thanks!
>> Chinh
>>    targets <- readTargets()
>>    targets
>>                        files groups description
>> 1     S3WT_tophatcount.txt     CT         TAM
>> 2     S4WT_tophatcount.txt     CT         TAM
>> 3 S1lrh1KO_tophatcount.txt     KO         TAM
>> 4 S2lrh1KO_tophatcount.txt     KO         TAM
>>> y <- readDGE(targets)
>> Warning messages:
>> 1: In `$.data.frame`(x$samples, group) :
>>     Name partially matched in data frame
>> 2: In `$.data.frame`(x$samples, group) :
>>     Name partially matched in data frame
>
> If you look at ?readDGE, under the files argument, there is this:
>
> files: character vector of filenames, or alternatively a data.frame
>             with a column containing the file names of the files
>             containing the libraries of counts and, optionally, columns
>             containing the ‘group’ to which each library belongs,
>             descriptions of the other samples and other information.
>
> And what that means is that a column labeled 'group' will be used to say
> which group the library belongs to. Since you have a column labeled
> 'groups', R is matching to that, and giving you a warning to let you
> know that it is matching to something that isn't an exact match, in case
> it isn't what you want. If you change the targets file to have a 'group'
> column, the warnings will go away.
>
> Best,
>
> Jim
>
>
>
>
>>
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>>
>> UT Southwestern Medical Center
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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