Dear list,

I try to run gcrma using the affinity computation without taking into
account MM probes i.e. by using the compute.affinities2 function as in

if(require(affydata) & require(hgu95av2probe) & require(hgu95av2cdf)){

     data(Dilution)

     ai <- compute.affinities2(cdfName(Dilution))

     Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities")

}



Unfortunately, the above results in



>     ai <- compute.affinities2(cdfName(Dilution))

Computing affinities.Done.

Warning message:

xy2i is deprecated and will be removed in the next BioC release.

Use xy2indices in the affy package instead.

>     Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities")

Adjusting for optical effect....Done.

Error in .local(object, ...) : subscript out of bounds

> traceback()

6: .local(object, ...)

5: mm(affinity.info)

4: mm(affinity.info)

3: gcrma.engine(pms = pm(object), mms = mm(object), ncs, pm.affinities = pm(
affinity.info),

       mm.affinities = mm(affinity.info), anc, type = type, k = k,

       stretch = stretch, correction = correction, GSB.adjust = GSB.adjust,

       rho = rho, verbose = verbose, fast = fast)

2: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source =
affinity.source,

       NCprobe = NCprobe, type = type, k = k, stretch = stretch,

       correction = correction, GSB.adjust = GSB.adjust, rho = rho,

       optical.correct = optical.correct, verbose = verbose, fast = fast)

1: gcrma(Dilution, affinity.info = ai, type = "affinities")



Am I overlooking something which explains the error above ?



Many thanks in advance,

Marianne



P.S.



> sessionInfo()

R version 2.8.1 (2008-12-22)

x86_64-unknown-linux-gnu



locale:

LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C



attached base packages:

[1] splines   tools     stats     graphics  grDevices utils     datasets

[8] methods   base



other attached packages:

[1] hgu95av2cdf_2.3.0   hgu95av2probe_2.3.0 affydata_1.11.5

[4] gcrma_2.14.1        matchprobes_1.14.1  affy_1.20.2

[7] Biobase_2.2.2       JavaGD_0.5-2        rJava_0.6-2



loaded via a namespace (and not attached):

[1] affyio_1.10.1        preprocessCore_1.4.0

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