Dear all: I'm trying to use limma package. But my intensity data is not two- colored, but single color(gray), like the following: Gene1 2596.87 2429.06 2436.62 2716.21 2508.85 2391.20 2515.86 2583.28 Gene2 1083.47 1071.37 1087.75 1022.47 1144.77 1078.31 1007.18 841.17 How should I do the normalization in Limma? Any guidance is appreciated. Chunrong

At 03:05 AM 19/08/2003, cxd55@cwru.edu wrote: >Dear all: > >I'm trying to use limma package. But my intensity data is not two- colored, >but single color(gray), like the following: > >Gene1 2596.87 2429.06 2436.62 2716.21 2508.85 2391.20 > 2515.86 2583.28 >Gene2 1083.47 1071.37 1087.75 1022.47 1144.77 1078.31 > 1007.18 841.17 > > >How should I do the normalization in Limma? Any guidance is appreciated. You need to read the data first into a data frame or a matrix, call it 'x'. I will assume that you have done this using 'read.table' or 'read.matrix'. You also need to make sure that there are no negative or zero intensities. If there are, then you should add a small constant to the negative intensities to make them positive. Then library(limma) e <- log(x,2) e <- normalizeQuantiles(e) This implements quantile normalization for the single-channel data and produces normalized expression values on the log-2 scale. Gordon >Chunrong > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

At 03:05 AM 19/08/2003, you wrote: >Dear all: > >I'm trying to use limma package. But my intensity data is not two- colored, >but single color(gray), like the following: > >Gene1 2596.87 2429.06 2436.62 2716.21 2508.85 2391.20 > 2515.86 2583.28 >Gene2 1083.47 1071.37 1087.75 1022.47 1144.77 1078.31 > 1007.18 841.17 > > >How should I do the normalization in Limma? Any guidance is appreciated. See also https://www.stat.math.ethz.ch/pipermail/bioconductor/2003-June/0017 72.html for a little more discussion. Cheers Gordon >Chunrong