[BioC] readDGE

James W. MacDonald jmacdon at uw.edu
Thu Jun 12 21:49:01 CEST 2014

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.



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

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