Question: basic limma questions
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gravatar for Gordon Smyth
11.4 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:
Dear Endre, It sounds as if limma recognised the ArrayVision format fine. As far as I know, there is no way to tell from the ArrayVision file which channel is cy3 and which is cy5. Even though limma got them the wrong way around in this case, it doesn't really matter because it makes no difference to the analysis. The Data-Ctrl contrast is the same regardless of which is R and which is G. Best wishes Gordon On Mon, 31 Mar 2008, Endre Sebestyen wrote: > Thanks for your answer. A little more details : > > I had a control and a treatment, with 3 technical replicates and no > dye-swaps. Cy3 was the treated, Cy5 the untreated. > > The ArrayVision result file looks like this : > > Ctrl Ctrl Ctrl Data Data > Data > Spot labels VOL - MDC Bkgd sVOL VOL - MDC Bkgd > sVOL Ratio (sVOL): Data / Ctrl Diff (sVOL): Data - Ctrl > MZ00023554 - TC248295 (1) 87573.5998 29969.817 > 57603.783 51217.7619 15349.622 35868.140 0.623 > -21735.643 > MZ00023408 - TC248006 (1) 29389.2252 29831.153 0.000 > 15896.2700 15349.622 546.648 1.0000e+100 546.648 > > I extracted the ID, Ctrl VOL, Ctrl Bkgd, Data VOL, Data Bkgd columns. > When I used the read.maimages function, Ctrl VOL became R, Data VOL > became G, Ctrl Bkgd became Rb, DataBkgd became Gb. > > Endre > >> > Date: Fri, 28 Mar 2008 12:51:39 +0100 >> > From: "Endre Sebestyen" <endre.sebestyen at="" gmail.com=""> >> > Subject: [BioC] basic limma questions >> > To: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> >> > >> > First, limma didn't recognize the ArrayVision format, and I had to >> > parse the raw data and define the columns myself. Is it correct to >> > pass the CtrlVol to R, DataVol to G, etc?
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ADD COMMENTlink modified 11.4 years ago by Endre Sebestyen60 • written 11.4 years ago by Gordon Smyth38k
Answer: basic limma questions
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gravatar for Endre Sebestyen
11.4 years ago by
Endre Sebestyen60 wrote:
Dear Gordon, Thanks for the answers. I have one final question. It is true that the Data-Ctrl contrast is the same in both cases, but it makes a difference if my gene is 10x up or 0.1x downregulated compared to the untreated sample. So either I have to change R and G, or use a design <- c(-1,-1,-1). Am I right? Endre On Tue, Apr 1, 2008 at 2:19 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > Dear Endre, > > It sounds as if limma recognised the ArrayVision format fine. As far as I > know, there is no way to tell from the ArrayVision file which channel is > cy3 and which is cy5. Even though limma got them the wrong way around in > this case, it doesn't really matter because it makes no difference to the > analysis. The Data-Ctrl contrast is the same regardless of which is R and > which is G. > > Best wishes > Gordon
ADD COMMENTlink written 11.4 years ago by Endre Sebestyen60
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