questions about MVA plot and loess N
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@phguardiolaolcom-152
Last seen 9.6 years ago
Hi, few questions: 1- could it be possible to get the IQR values separately when using the mva.pairs function ? That would be useful if a large number of chips are run at the same time and one wants to compare the different normalization methods ? 2- is there a way to modify the name of the chip inside the MA plot ? 3- should I care about getting with loess normalization the following warning message: k-d tree limited by memory . ncmax=5002 9exact process was: data2 <- expresso(data, normalize.method="loess", bgcorrect.method="rma", summary.method="medianpolish", pmcorrect.method="pmonly") 4- where can I find more informaiton about the different summary.method available in affy ? some are completely unkown to me and I d like to learn about these 5- about normalization what I have understood is that some tools like MA plots can tell you that you have not "normalized enough" your data, but is there a way to see that you have gone too far with the process ? Maybe that s a stupid question....sorry ! thanks for your help anyway Philippe
Normalization affy Normalization affy • 822 views
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@rafael-a-irizarry-205
Last seen 9.6 years ago
On Wed, 25 Jun 2003 Phguardiol@aol.com wrote: > Hi, > few questions: > 1- could it be possible to get the IQR values separately when using the mva.pairs function ? That would be useful if a large number of chips are run at the same time and one wants to compare the different normalization methods ? you can use, for example, a for loop and the function IQR > 2- is there a way to modify the name of the chip inside the MA plot ? read the man page. > 3- should I care about getting with loess normalization the following warning message: k-d tree limited by memory . ncmax=5002 9exact process was: data2 <- expresso(data, normalize.method="loess", bgcorrect.method="rma", summary.method="medianpolish", pmcorrect.method="pmonly") no. just warnings from the function loess. > 4- where can I find more informaiton about the different summary.method available in affy ? some are completely unkown to me and I d like to learn about these the help files and vignette have some references. > 5- about normalization what I have understood is that some tools like MA plots can tell you that you have not "normalized enough" your data, but is there a way to see that you have gone too far with the process ? Maybe that s a stupid question....sorry ! > thanks for your help anyway > Philippe not stupid question at all. its hard when you dont have some genes for which you now there should be a difference. for more on this read the 2003 bioinformatics paper by bolstad et al. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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