If you know that a group of genes are not expressed (for example, Y 
chromosome genes in a female sample, or cell-type / tissue specific 
genes), you can use the value of those genes to determine your cutoff. 
It's not really algorithm (MAS or RMA) dependent.

Michael

On 07/07/2010 6:28 AM, Hernando Martínez wrote:
> Hi, I need to remove genes with low expression values from a expression
> matrix. I would like to remove those with an average of expression values
> less than a certain cut-off. I was thinking in computing the average for
> each row, create a list with the gene names for which their average is less
> than the cut-off, and remove those genes from the initial matrix. However, I
> have a couple of doubts that maybe you can help me with. Is there any
> package or function that makes this easier? And, does anyone know which
> cut-off to use for data normalized with RMA and for data normalized with
> MAS5? Thanks,
>
>
>    
>
>
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