[BioC] readDGE
Chinh Hoan
Chinh.Hoang at utsouthwestern.edu
Thu Jun 12 21:55:04 CEST 2014
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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James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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