normalization of a data frame
1
0
Entering edit mode
joseph ▴ 330
@joseph-1270
Last seen 10.3 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080211/ 0c339153/attachment.pl
• 679 views
ADD COMMENT
0
Entering edit mode
joseph ▴ 330
@joseph-1270
Last seen 10.3 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080211/ 0c339153/attachment-0001.pl
ADD COMMENT
0
Entering edit mode
Hi, one option is to use the normalization methods in 'aroma.light', which take matrices (or lists) containing signals on the intensity scale (non-logged signals), so you could do: library(aroma.light) X <- as.matrix(df) and pick one of: Xn <- normalizeAverage(X) Xn <- normalizeQuantile(X) Xn <- normalizeCurveFit(X) followed by dfN <- as.data.frame(Xn) For normalizeCurveFit() you can specify either method="loess" (default/slowest), "lowess", "spline", or "robustSpline". See help(aroma.light) for more details and help(normalizeCurveFit.matrix) for an example. Hope this helps /Henrik PS. I'll add it to the to do list for the next release to add normalization wrappers for data.frame:s as well so you don't have to do the above coercions. DS. On Feb 11, 2008 11:26 PM, joseph <jdsandjd at="" yahoo.com=""> wrote: > > > Hi > > I have a data frame that looks like the one below. I would like to apply to its columns the different > kinds of normalizations such as median global normalization (Scaling), Quantile > Normalization, and Lowess. Do I have to use packages such as affy, Limma and > marray and if so what do I have to do to the data frame in order to be able to > analyze it with these packages? > > > Thanks > > > > > > df=data.frame (row.names=LETTERS[1:10], col1=c(1,4,7:9,2:6), > col2= c(1:4,9, 10:14), col3=c(14,6:10,8:11)) > > > > df > > > col1 col2 col3 > > > A 1 1 > 14 > > > B 4 2 > 6 > > > C 7 3 > 7 > > > D 8 4 > 8 > > > E 9 9 > 9 > > > F 2 10 > 10 > > > G 3 11 > 8 > > > H 4 > 12 9 > > > I 5 13 > 10 > > > J 6 14 > 11 > > > > > > > > > > > > > ______________________________________________________________ ______________________ > Looking for last minute shopping deals? > > [[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 >
ADD REPLY

Login before adding your answer.

Traffic: 606 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