[BioC] mas5call select genes

[Stephen Henderson]

On a slight tangent...

Is there really any point using the MAS5 calls in any case as though a
useful quality control for the whole experiment singly they seem to have a
poor sensitivity/specificity? If you use a variance based filter i.e.
filtering all data below a given coefficient of variance this should remove
non-expressed data  (and inherently uninteresting data depending upon the
experiment and design) as it should not vary by much more than the baseline.

This is what I do but if anyone thinks this is wrong (or right) I'm
interested to know??





-----Original Message-----
From: Claire Wilson
To: Katleen De Preter
Cc: bioconductor at stat.math.ethz.ch
Sent: 1/13/05 8:49 AM
Subject: RE: [BioC] mas5call select genes

Hi Katleen,

This is the function I use on a matrix of Affymetrix Absent/Present
calls (rows are probesets, columns are chips)


number.pres <- function(x) {
	x[x=="P"] <- 1;
	x[x!=1]   <- 0;
	return(apply(x,1,function(a) { sum(as.integer(a))}))
}

# Calculate present/absent calls
# They are stored in the exprs slot of PAcalls
PAcalls <- mas5calls(raw.data)

# This returns a vector where each probeset is listed with the total
number of present calls
np <- number.pres(PAcalls at exprs)

# Get those probesets with at least 1 present call
my.list <- names(np[np>0])

The simpleaffy library also provides a function (pairwise.filter) to
filter Affymetrix data and one of the parametres allows you to specify a
minimum number of chips on which a probeset must be called present

Hope this helps

Claire

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Katleen De Preter
> Sent: 13 January 2005 08:08
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] mas5call select genes
> 
> Dear Colleagues,
> I would like to select genes based on the Affymetrix calls 
> (mas5call-function in affy package). For example, how can I 
> obtain the 
> list of genes/probeIds that have in at least 1 of 20 experiments a 
> present call?
> Best regards,
> Katleen De Preter
> 
> 
> 
> 
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