Hi Yogi,
have you tried reading both files with 'lumiR' and then combining the
resulting LumiBatch objects with 'combine'?
See help for:
?lumiR
?LumiBatch
?combine
This should work fine as long as none of the samples have duplicated
names.
Cheers,
Cei
On Mon, 24 Sep 2007, Yogi Sundaravadanam wrote:
> Hi all
>
>
>
> I have got 2 sample gene profile files (18 illumina samples in each)
and
> I would like to analyse them together in lumi. Is this possible? I
just
> thought I?d copy-paste contents of one file into another, but there
> aren?t sufficient columns in Excel to accommodate this
concatenation.
>
>
>
> I was thinking may be I should edit the files to isolate columns
that
> are really necessary but I was just wondering if there is a simple
way
> to do this, as my knowledge of R is pretty challenged.
>
>
>
>
>
> Cheers
>
> Yogi
>
>
>
> [[alternative HTML version deleted]]
>
>
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
Hi Yogi,
You can input the data files separately and then using combine()
function to
combine the data. Also I just added a new function: lumiR.batch, which
can
input multiple data files together. You can have a try.
Pan
On 9/24/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at="" stat.math.ethz.ch=""> wrote:
> Message: 2
> Date: Mon, 24 Sep 2007 16:14:49 +1000
> From: "Yogi Sundaravadanam" <yogi.sundaravadanam at="" agrf.org.au="">
> Subject: [BioC] Analysis of two sample gene files in lumi
> To: bioconductor <bioconductor at="" stat.math.ethz.ch="">
> Message-ID: <h000029400321fec.1190614488.mailmaster.agrf.org.au at="" mhs="">
> Content-Type: text/plain
>
> Hi all
>
>
>
> I have got 2 sample gene profile files (18 illumina samples in each)
and
> I would like to analyse them together in lumi. Is this possible? I
just
> thought I?d copy-paste contents of one file into another, but there
> aren?t sufficient columns in Excel to accommodate this
concatenation.
>
>
>
> I was thinking may be I should edit the files to isolate columns
that
> are really necessary but I was just wondering if there is a simple
way
> to do this, as my knowledge of R is pretty challenged.
>
>
>
>
>
> Cheers
>
> Yogi
