Question: limma Agilent Normalization
0
gravatar for Noemi Andor
9.1 years ago by
Noemi Andor100
Noemi Andor100 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") 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 • 809 views
ADD COMMENTlink modified 9.1 years ago by Sean Davis21k • written 9.1 years ago by Noemi Andor100
Answer: limma Agilent Normalization
0
gravatar for Sean Davis
9.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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 COMMENTlink written 9.1 years ago by Sean Davis21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 269 users visited in the last hour