[BioC] single color microarray analysis

[zhihua li]

Hi netters!

I would like to know if there r any packages in bioconductor that can 
perform single-color
microarray analysis on the gene level instead of the probe level. That's to 
say, I've had a matrix with each column representing the expression values 
for a list of genes in a given condition and each row represents the 
expression value of a gene across different conditions. I wanna do all the 
analysis like normalization, plotting....etc. I was at a loss what packages 
should I use?  The affy package generally handles probe-level data - they 
require the colomns to be signals for PM and MM probes, not the expression 
level of genes. The limma package provides some tools to analysis my data, 
such as normalizeQuantiles, etc. But limma generally handles two-color 
microarray data, so there's not much can be done with my data. For example, 
limma's plotting functions usually require both Red and Green signal 
levels. I'm a bit surprised to see that there seems no packages to handle 
single-color microarray data on the gene level. Could anyone help me?  
Thanks a lot!