[BioC] expresso error

[Vincent Carey]

I reproduced your experience.  The problem is that the software lets
you get away
with not specifying the summary.method and the pmcorrect.method at the
interface, but
when it gets around to doing the expression computations, if it gets
NULLs (the default)
it dies.  expresso() should probably force the user to put something
in or put reasonable
defaults.

if you add summary.method = "avgdiff" and pmcorrect.method="pmonly" to
your call, for example,
it will complete.  you have to look over the options for those
methods; the doc is not crystal
clear in all places.  for some parameters function calls will tell you
the options available

> bgcorrect.methods()
[1] "bg.correct" "mas"        "none"       "rma"
> pmcorrect.methods()
[1] "mas"        "methods"    "pmonly"     "subtractmm"

summary.methods() does not seem to exist.  but

> generateExprSet.methods()
[1] "avgdiff"      "liwong"       "mas"          "medianpolish" "playerout"

seems to supply the relevant options for that parameter.


On Wed, Oct 6, 2010 at 9:59 PM, ANJAN PURKAYASTHA
<anjan.purkayastha at gmail.com> wrote:
> Hi Vincent,
> I used the Mouse Genome 430 2.0 Array
> (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20)
>
> Here is my session info:
> R version 2.11.1 (2010-05-31)
> i386-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mouse4302cdf_2.6.0 simpleaffy_2.24.0  gcrma_2.20.0
> genefilter_1.30.0  affy_1.26.1        Biobase_2.8.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.16.0         annotate_1.26.1       AnnotationDbi_1.10.2
> Biostrings_2.16.9     DBI_0.2-5             IRanges_1.6.17
> preprocessCore_1.10.0
>  [8] RSQLite_0.9-2         splines_2.11.1        survival_2.35-8
> tools_2.11.1          xtable_1.5-6
>
> Thanks in advance for your help.
> Anjan
>
>
> On Wed, Oct 6, 2010 at 9:36 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>>
>> please provide your sessionInfo() and the specific class of array in
>> use -- there are various mouse
>> expression arrays from affy.
>>
>> On Wed, Oct 6, 2010 at 9:17 PM, ANJAN PURKAYASTHA
>> <anjan.purkayastha at gmail.com> wrote:
>> > Hi,
>> > I have created an affybatch object from 3 cel files. The files have data
>> > from Affymetrix's Mouse Expression (Oligonucleotide) array.
>> > Affybatch object was created by command:
>> > testAffy <- ReadAffy()
>> >
>> > In the next step I tried to use expresso to adjust background using RMA
>> > and
>> > normalize using loess, using the command:
>> > testAffy.loess = expresso(testAffy, bgcorrect.method= "rma",
>> > normalize.method= "loess")
>> > Here is the output:
>> > background correction: rma
>> > normalization: loess
>> > PM/MM correction :
>> > expression values:
>> > background correcting...done.
>> > normalizing...Done with 1 vs 2 in iteration 1
>> > Done with 1 vs 3 in iteration 1
>> > Done with 2 vs 3 in iteration 1
>> > 1 0.0176947
>> > done.
>> > Error in function (classes, fdef, mtable)  :
>> >  unable to find an inherited method for function "computeExprSet", for
>> > signature "AffyBatch", "NULL", "NULL"
>> >
>> > The testAffy.loess object was not created.  Any idea why I am getting an
>> > error on running the expresso command?
>> > Thanks in advance.
>> > Anjan
>> >
>> > --
>> > ===================================
>> > anjan purkayastha, phd.
>> > research associate
>> > fas center for systems biology,
>> > harvard university
>> > 52 oxford street
>> > cambridge ma 02138
>> > phone-703.740.6939
>> > ===================================
>> >
>> >        [[alternative HTML version deleted]]
>> >
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>
>
>
> --
> ===================================
> anjan purkayastha, phd.
> research associate
> fas center for systems biology,
> harvard university
> 52 oxford street
> cambridge ma 02138
> phone-703.740.6939
> ===================================
>