Quantile normalization in Ringo package
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@mohamed-lajnef-3515
Last seen 8.1 years ago
Dear all I'd like to use quantile ( not Rquantile or Gquantile) normalization in preprocess function in Ringo package, it's possible to do that ? Any help would be appreciated Regards M -- #################################### Mohamed Lajnef,IE INSERM U955 eq 15# Pôle de Psychiatrie # Hôpital CHENEVIER # 40, rue Mesly # 94010 CRETEIL Cedex FRANCE # Mohamed.lajnef@inserm.fr # tel : 01 49 81 31 31 (poste 18467) # Sec : 01 49 81 32 90 # fax : 01 49 81 30 99 # #################################### [[alternative HTML version deleted]]
Ringo Ringo • 858 views
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Noah Dowell ▴ 410
@noah-dowell-3791
Last seen 8.1 years ago
Hello Mohamed, Did you read the help page for normalize.Probes? Quantile normalization can be done like this: normalize.Probes(eset, method= "quantile") best, noah On Sep 24, 2010, at 9:41 AM, Mohamed Lajnef wrote: > Dear all > > I'd like to use quantile ( not Rquantile or Gquantile) normalization in > preprocess function in Ringo package, it's possible to do that ? > Any help would be appreciated > Regards > M > > -- > #################################### > Mohamed Lajnef,IE INSERM U955 eq 15# > P?le de Psychiatrie # > H?pital CHENEVIER # > 40, rue Mesly # > 94010 CRETEIL Cedex FRANCE # > Mohamed.lajnef at inserm.fr # > tel : 01 49 81 31 31 (poste 18467) # > Sec : 01 49 81 32 90 # > fax : 01 49 81 30 99 # > #################################### > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@joern-toedling-3465
Last seen 8.1 years ago
Hi, you can use the 'normalizeBetweenArrays' function from package limma with method="quantile" on your RGList and then convert the resulting MAList using the function asExprSet from the Ringo package. Please check the source code of "preprocess", as it does the same thing for other methods. So it's possible, but you will have to decide whether this kind of strong normalization is appropriate with your data. Regards, Joern On Fri, 24 Sep 2010 18:41:51 +0200, Mohamed Lajnef wrote > Dear all > > I'd like to use quantile ( not Rquantile or Gquantile) > normalization in preprocess function in Ringo package, it's > possible to do that ? Any help would be appreciated Regards M > > -- > #################################### > Mohamed Lajnef,IE INSERM U955 eq 15# > P?le de Psychiatrie # > H?pital CHENEVIER # > 40, rue Mesly # > 94010 CRETEIL Cedex FRANCE # > Mohamed.lajnef at inserm.fr # > tel : 01 49 81 31 31 (poste 18467) # > Sec : 01 49 81 32 90 # > fax : 01 49 81 30 99 # > #################################### > > [[alternative HTML version deleted]] --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246927
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