[BioC] mas5call select genes

[Rafael Irizarry]

rowSums(x=="P")

does the same as number.pres below. this type of calculation is my 
favorite strength of R (actually the S language in general).

On Jan 13, 2005, at 3:49 AM, Claire Wilson wrote:

> 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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