________________________________________ 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 [EMAIL PROTECTED] ________________________________________ From: jim holtman [EMAIL PROTECTED] Sent: Wednesday, July 23, 2008 7:15 AM To: Kaposi-Novak, Pal Cc: r-help@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 <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] > > ______________________________________________ > R-help@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? ______________________________________________ R-help@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.
