[BioC] Replace method, AffyBatch, pm or mm

[laurent buffat]

Hi, 

Thanks for Raphael, Robert & Laurent for your answers. It helps me to solve
my problem:

I work with R 1.9.0 and affy 1.5.0, but:

Historically, to get a probe intensity of a probe set name, I used an old
"signature" of pm: pm( aBatch, aProbeSetName)

This is not supported any more with affy >= 1.5.0) and then you try to use
it you have this error :

#  R version : 1.9.0
> library(affy)
> package.version("affy")
# 1.5.0
> data(affybatch.example)      

> psn <-  "A28102_at"
> chips <- c("20A","20B")

> pm(affybatch.example,psn) [, chips] 
Error in .local(object, which, ...) : couldn't find function "multiget"

Because, I have write some code with this "old call" and I would like to
continue to use it and I not understood the "intensity method", I try to
correct these error and "manually" restore the "multiget" function

> source("/somewhere/multi.R") 

With an old definition of multi.R and these definition use mget, but its
works (with warning) and I was able to get the "intensity" of a probeset in
a batch with the "old signature of pm" :

> pm(affybatch.example,psn) [, chips]
              20A   20B
A28102_at1  149.0 118.0
A28102_at2  143.5 124.8
A28102_at3  132.0 111.0
A28102_at4  130.0  98.0
A28102_at5  115.8 114.3
A28102_at6  131.0 143.0
A28102_at7  131.8 124.0
A28102_at8  140.0 129.0
A28102_at9  122.0 172.0
A28102_at10 133.3 178.0
A28102_at11 136.0 145.8
A28102_at12 123.0 138.0
A28102_at13 132.5 131.0
A28102_at14 130.0 113.8
A28102_at15 125.0 119.0
A28102_at16 133.5 164.0
Warning message:
'multiget' is deprecated.
Use 'mget' instead.
See help("Deprecated") and help("base-deprecated").


And so, I continued to use it. That I have not understood, and I apologize
for this, is that with the new version of affy, I have to use "intensity"
and ProbesIndex do to what I try to do :

Instead of "pm(aBatch, aProSetName)" to get or replace intensity of probes
of a probeset in a affybatch, I have to use Intensity & probesIndex :


>xi <- intensity(affybatch.example)[
indexProbes(affybatch.example,"pm")[[psn]],chips]

instead of

> xi <- pm(affybatch.example,psn)[,chips]

And to REPLACE :

>intensity((affybatch.example)[
indexProbes(affybatch.example,"pm")[[psn]],chips]) <- NA

Instead of

>pm(affybatch.example.psn)[,chips] <- NA


Thanks again for your help and sorry for the confusion.


Laurent Buffat


-----Message d'origine-----
De : bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] De la part de Laurent
Gautier
Envoye : mercredi 20 octobre 2004 05:22
A : rafa at jhu.edu
Cc : Laurent Buffat; Laurent Gautier; Robert Gentleman;
bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] Replace method, AffyBatch, pm or mm

Rafael A. Irizarry wrote:

> as far as i know all the multigets where removed some time ago. what
> version are you using? if you find a multiget in >=1.5 please let me know.

'multiget' was removed for the last release, both in the code and in the 
doc...

Apparently only one was forgotten (and still is) in the text of a 
vignette...


I believe that the user has an old version of the package...

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