[BioC] Problems in MAplot for affybatch objects

[Javier Pérez Florido]

Dear Ben,
I've installed the new version of both R and affyPLM package (1.24), but 
the problem is still there....
Thanks,
Javier


On 10/04/2010 21:51, Ben Bolstad wrote:
> Hi Javier,
>
> You have indeed found discrepant behavior that should be fixed. MAplot
> for ExpressionSet object is implemented in affyPLM, MAplot for AffyBatch
> objects is implemented in affy. So it is not really the same set of code
> being executed in each case. But the basic behavior was intended to be
> harmonious between the two. I will fix.
>
> Ben
>
>
>
>
> On Sat, 2010-04-10 at 16:47 +0200, Javier Pérez Florido wrote:
>    
>> Dear list,
>> I am trying to use MAplot (affyPLM packages) using 2 arrays for the
>> argument 'which' and the same arrays for the argument 'ref'.
>> So
>>
>> /library(affyPLM)
>> library(affydata)
>> data(Dilution) # Dilution data set
>> par(mfrow=c(2,1),1)
>> MAplot(Dilution,which=c(1,3),ref=c(1,3),plot.method="smoothScatter") /
>>
>> I got the following warnings
>>
>> /Warning messages
>> 1: In if (i != ref) { :
>>     the condition has length>  1 and only the first element will be used
>> 2: In if (i != ref) { :
>>     the condition has length>  1 and only the first element will be used/
>>
>> The reference mean array is not built and, thus, the MAplot is not correct
>> However, the same piece of code on an expression set object works:
>> /
>> eset<-threestep(Dilution)
>> par(mfrow=c(2,1),1)
>> MAplot(eset,which=c(1,3),ref=c(1,3),plot.method="smoothScatter")/
>>
>> What's the problem on affybatch objects?
>> Thanks in advance,
>> Javier
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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>
>
>