limma Agilent Normalization
1
0
Entering edit mode
Noemi Andor ▴ 100
@noemi-andor-4128
Last seen 8.0 years ago
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="">
Normalization CGH Normalization CGH • 1.0k views
ADD COMMENT
0
Entering edit mode
@sean-davis-490
Last seen 3 months ago
United States
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]]
ADD COMMENT

Login before adding your answer.

Traffic: 573 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6