Hi, I'm working with the Agilent CGH 244A Platform, and I normalized the data using the command: MA <- normalizeWithinArrays(Agilent.RG, method="loess") Than I made MA plots: plotMA3by2(Agilent.RG) vs. plotMA3by2(MA ) Yet I get the same plots, i.e. normalization had no effect upon the data (see attached plots). I read something about weightening particular spots within the normalization, would that be a solution, considering the attached plots? I would also like to have a fitting curve in each plot. I read the command: plotPrintTipLoess(RG) would create such plot, but here I get the error that some layout object is missing (ngrid.r, ngrid.c - number of grid rows/columns on the arrays - do not know where to extract that information) Or is there any other solution to do this? -------------- next part -------------- A non-text attachment was scrubbed... Name: MA-1-6_afterNorm.png Type: image/png Size: 32545 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100619="" ada4985c="" attachment.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: MA-1-6_beforeNorm.png Type: image/png Size: 32118 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100619="" ada4985c="" attachment-0001.png=""> -------------- next part -------------- A non-text attachment was scrubbed... Name: MA-1-6_beforeNorm.png Type: image/png Size: 32118 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100619="" ada4985c="" attachment-0002.png="">

On Sat, Jun 19, 2010 at 1:27 AM, Noemi Andor <noemi.andor@campus.lmu.de>wrote: > Hi, > > I'm working with the Agilent CGH 244A Platform, and I normalized the data > using the command: > MA <- normalizeWithinArrays(Agilent.RG, method="loess") > > Hi, Noemi. You do not want to be normalizing CGH arrays using loess normalization, I do not think. > Than I made MA plots: > > plotMA3by2(Agilent.RG) vs. plotMA3by2(MA ) > > Best to include the exact code that you are using and the output of sessionInfo(). > Yet I get the same plots, i.e. normalization had no effect upon the data > (see attached plots). > I read something about weightening particular spots within the > normalization, would that be a solution, considering the attached plots? > > I would also like to have a fitting curve in each plot. I read the command: > > plotPrintTipLoess(RG) > > would create such plot, but here I get the error that some layout object is > missing (ngrid.r, ngrid.c - number of grid rows/columns on the arrays - do > not know where to extract that information) > > Or is there any other solution to do this? > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]