Dear Bioconductor List,

I am doing two color Agilent microarray analysis by limma.

I tried to normalize* M *values by using following command.But both the
commands are giving different M values.

*(1) MA<- normalizeBetweenArrays (MAw, method="quantile")

*
*(2) MA <- **normalizeBetweenArrays (MAw$M, method="quantile")

*
the first command does not give same boxplot of M value for all arrays ,
but second command is giving same boxplot for all arrays.*

*
*I want to know whether first command is proper for between the array
normalization and is it applied on M values or not?

*
Thanks *
*
*
**
*

--

	[[alternative HTML version deleted]]

