[BioC] removal of genes with low expression values

Robert Castelo robert.castelo at upf.edu
Thu Jul 8 13:16:16 CEST 2010


Hernando,

if by removing genes with low expression values you mean removing genes
that are not expressed or have an undetectable level of expression with
the microarray instrument employed, the issue is not as easy as it may
look like if you need to do it very accurately because different genes
may behave differently due to complicated probe-specific effects.

i would encourage you to take a look at this publication:

Zilliox MJ, Irizarry RA
A gene expression bar code for microarray data.
Nat Methods. 2007 Nov;4(11):911-3.
http://www.ncbi.nlm.nih.gov/pubmed/17906632
http://rafalab.jhsph.edu/barcode


i'm not the authority about this, and the authors of the work could give
you a more specific advice, but i'd say that the take-home message is
that if you have a sufficiently large panel of biological replicates for
a variety of cellular states, try to use them to find a gene-dependent
threshold of expression under the assumption that only a small fraction
of genes is expressed under a specific cellular state.

cheers,
robert.



On Wed, 2010-07-07 at 11:28 +0100, 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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