[R] FW: average replicate probe values

From: Kaposi-Novak, Pal <kaposinovakp_at_upmc.edu>
Date: Wed, 23 Jul 2008 17:08:14 -0400



From: Kaposi-Novak, Pal
Sent: Wednesday, July 23, 2008 5:07 PM
To: jim holtman
Subject: RE: [R] average replicate probe values

Dear Dr Holtman,

Thank you very much for your response.

What I want is avarege data points in a data.frame from probes which represent the same gene (ie have the same UniGene ID).

For example in the table below probe sets in rows 3 and 4 both represent the CEP57 gene.

UNIQID UniGene Gene 1_SL 2_SL 17_SL 18_SL 38_ SL

1175390 Hs.10095 MLLT1 -0.00595 0.62315 0.85315 1.11215 -0.195
1175392 Hs.10101 C1orf166 -0.4945 -0.04025 0.1299 -0.00575 -0.1824
1187428 Hs.101014 CEP57 0.60085 0.2564 -0.42885 -0.57635 -0.14735
1193447 Hs.101014 CEP57 -0.15625 -0.1681 -0.4891 -0.29995 NA
1173756 Hs.1011 PROZ -0.7211 -0.68895 0.4651 0.30815 0.1133

I would like to make R find the matching UniGene IDs and average expression values for each sample. The result would look like the table below:

UNIQID UniGene Gene 1_SL 2_SL 17_SL 18_SL 38_ SL

1175390 Hs.10095 MLLT1 -0.00595 0.62315 0.85315 1.11215 -0.195
1175392 Hs.10101 C1orf166 -0.4945 -0.04025 0.1299 -0.00575 -0.1824
1199466 Hs.101014 CEP57 0.2223 0.04415 -0.458975 -0.43815 -0.14735
1173756 Hs.1011 PROZ -0.7211 -0.68895 0.4651 0.30815 0.1133

I am sorry for the naivness of my question, but I am not a trained biostatistician just need to analyze data.

Sincerely,

Pal Kaposi-Novak MD PhD
PIRT Fellow
University of Pittsburgh
Department of Pathology
BST S408, 200 Lothrop Str
Pittsburgh, PA , 15261
Tel: (412) 383-7748
kaposinovakp_at_umpc.edu



From: jim holtman [jholtman_at_gmail.com]
Sent: Wednesday, July 23, 2008 7:15 AM
To: Kaposi-Novak, Pal
Cc: r-help_at_r-project.org
Subject: Re: [R] average replicate probe values

It would be helpful if you included a sample of the data so that we could understand what you would like to do with it (before/after pictures).

?aggregate

On Tue, Jul 22, 2008 at 9:57 PM, Kaposi-Novak, Pal <kaposinovakp_at_upmc.edu> wrote:
> Hi,
>
> Could somebody tell me how I can average expression values of replicate probe sets in an data frame?
>
> Thanks
>
> Pal Kaposi-Novak MD PhD
> PIRT Fellow
> University of Pittsburgh
> Department of Pathology
> BST S408, 200 Lothrop Str
> Pittsburgh, PA , 15261
> Tel: (412) 383-7748
> kaposinovakp_at_umpc.edu
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem you are trying to solve?

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Received on Wed 23 Jul 2008 - 23:00:29 GMT

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