[BioC] GCRMA fails with MOE430A Only

[paul.boutros at utoronto.ca]

Hi again,

I'm analyzing an experiment that uses MOE430A chips on R1.9.1 and GCRMA 1.1.0 on 
a windows machine.  I get an error message from GCRMA of: 

> eset <- gcrma(eset);
Computing affinitiesError in get(x, envir, mode, inherits) : variable 
"moe430aprobe" was not found

> traceback();
3: get(probepackagename)
2: compute.affinities(cdfName(object), verbose = verbose)
1: gcrma(eset)

This issue does *not* occur with other chip-types (see below) and doesn't go 
away if I load the probe-library with library() (also see below).  The problem 
does not seem to depend on the specific CEL-files, as I have used over 40 
different files and they all seem to exhibit this problem.

Any suggestions on what might be going wrong here?  Any additional data I can/
should provide?

Paul



# Try to process MOE430A files
> cel.files <- c(
+ '2(1b)MOE430A_081904_MS01T_LH.CEL',
+ '2(2b)MOE430A_081904_MS02T_LH.CEL',
+ '2(3)MOE430A_012904_MS01T_LH.CEL',
+ '2(4)MOE430A_012904_MS02T_LH.CEL',
+ '2(5)MOE430A_012904_MS03T_LH.CEL',
+ );

> eset <- ReadAffy(filenames=cel.files);

> eset;
AffyBatch object
size of arrays=712x712 features (19806 kb)
cdf=MOE430A (22690 affyids)
number of samples=5
number of genes=22690
annotation=moe430a

> eset <- gcrma(eset);
Computing affinitiesError in get(x, envir, mode, inherits) : variable 
"moe430aprobe" was not found

> traceback();
3: get(probepackagename)
2: compute.affinities(cdfName(object), verbose = verbose)
1: gcrma(eset)

# Try to manually load probe library
> library(moe430aprobe);
> eset <- gcrma(eset);
Computing affinitiesError in get(x, envir, mode, inherits) : variable 
"moe430aprobe" was not found

# Try this on RAE230-2 arrays
> setwd("../test");
> eset <- ReadAffy();
> eset
Attaching package 'rat2302cdf':


        The following object(s) are masked from package:moe430acdf :

         i2xy xy2i 

AffyBatch object
size of arrays=834x834 features (16306 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=3
number of genes=31099
annotation=rat2302

# and it succeeds!
> eset <- gcrma(eset);
Computing affinities.Done.
Adjusting for optical effect...Done.
Adjusting for non-specific binding...Done.
Normalizing
Calculating Expression