Hello: I am analyzing farmer_breast data. I classified normals as normal and any other transformed tissue into cancer. in my class file CL0 = normal and CL1 = Cancer I wrote a function to compute fold changes. I would like some help from group members to comment on this function to calculate fold changes. 1. is there a better way to calculate. 2. how do i get log-fold changes. fc <- function(x,CL0,CL1){ x0 <- x[,CL0] x1 <- x[,CL1] res <- (apply(x0,1,mean) - apply(x1,1,mean)) } foldcs <-fc(mydata_mat,CL0=farm.cl==0),CL1=fram.cl==1)) logfoldcs <- log(foldcs,2) OR loggoldcs <- log2(foldcs) While doing this I get error: Warning message: NaNs produced in: log(x, base) Could any one help me please. Thanks sri

Srinivas Iyyer wrote: > Hello: > > I am analyzing farmer_breast data. I classified > normals as normal and any other transformed tissue > into cancer. > in my class file CL0 = normal and CL1 = Cancer > > > I wrote a function to compute fold changes. > I would like some help from group members to comment > on this function to calculate fold changes. > > 1. is there a better way to calculate. > 2. how do i get log-fold changes. > > > > > fc <- function(x,CL0,CL1){ > x0 <- x[,CL0] > x1 <- x[,CL1] > res <- (apply(x0,1,mean) - apply(x1,1,mean)) > } > > > foldcs > <-fc(mydata_mat,CL0=farm.cl==0),CL1=fram.cl==1)) > > > logfoldcs <- log(foldcs,2) OR loggoldcs <- > log2(foldcs) > > While doing this I get error: > Warning message: > NaNs produced in: log(x, base) Hi, Sri. Your fc() function does a subtraction. It seems like foldcs might have some negative values, for which log is undefined. A fold-change on non-logged raw expression (or ratio in two-color terms) is a ratio, not a difference. Sean