Hi.
Below is an outline of the code I am using to analyse two colour array data.
Normal = Cy3
Case = Cy5
There are 3 replicates.

Can the fold change be reported back in the siggenes.table? From the
documentation, it is not obvious how this is done.

Thank you for any help.





# Code for Two colour data normalised with maNorm. ########

data.normalised <- (two colour array matrix of data);

# Make column names 1, 2 and 3
colnames(data.normalised) <- seq(1:3);

# Make the row names gene names
rownames(data.normalised) <- gene_names;

library(impute);
# Replace nas with numbers
imputed<-impute.knn(data.normalised,k=3);

# Take the raw data from impute object
x<-imputed$data;

# One class, so a list of 1's
y<-c(rep(1,3));

# Prepare the samr data
data.sam <- list(x=x, y=y, genenames=rownames(data.normalised),
geneid=gene_names,logged2=T);

library(samr);

# Do the one class SAMR analysis
samr.obj <- samr(data.sam,resp.type="One class",nperms=100);

# Set up a delta value
delta=0.4

# Compute the delta table
delta.table <- samr.compute.delta.table(samr.obj)

# Collect the significant genes into a table
siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, data.sam,
delta.table);

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