[BioC] Exclude probes that show sd above 0.1 between replicatevalues

[J.delasHeras at ed.ac.uk]

If you look at the variation on M values alone (it's a MAList), and  
throw away those with high variation... that sounds like a reasonable  
thing to do, except that when you have spots with no signal in only  
one of the channels, the variation is probably quite high too, and  
you'd remove them. However, they are probably quite an interesting  
class of spots to keep (genes that become silenced, or activated,  
after treatment, not merely down/upregulated).

I'm mostly studying experiments when I am interested mostly in these  
cases of activation/silencing, and not so much in up/downregulation  
alone. I wonder how people account for these situations...

Jose

Quoting J.Oosting at lumc.nl:

> Hi João
>
> Here's how I did it on a set of arrays with 3 replicates. ID is a   
> column that has identical values for replicate spots.
>
> spotaverage<-function(x) {
>   # at max 1 NA, and have low variability
>   if (sum(is.na(x))<2 && sd(x,na.rm=TRUE)<0.1)  median(x,na.rm=TRUE)
>   else NA
> }
> aggcollumn<-function(x) {
>   agg<-aggregate(x,list(genes=MAn$genes[,"ID"]),FUN=spotaverage)
>   ac<-as.numeric(agg[,2])
>   names(ac)<-agg[,1]
>   ac
> }
>
> avg.m<-apply(MAn$M,2,aggcollumn)
>
>
>>
>> Dear list,
>>
>> I have a MAList and I want to exclude probes that show a
>> standard deviation above 0.1 between the replicate values.
>> The number of within-array replicates for each probe (ndups)
>> is equal to 2 and the number of spots to step from a probe to
>> its duplicate (spacing) is equal to 1.
>> I am not able to to this. Can somebody give me some a hint to
>> resolve this?
>>
>>
>> Best regards
>>
>> João Fadista
>> Ph.d. student
>>
>
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-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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