[BioC] expresso error

[Vincent Carey]

On Wed, Oct 6, 2010 at 10:46 PM, ANJAN PURKAYASTHA
<anjan.purkayastha at gmail.com> wrote:
> Vince,
> Thanks. So it looks like there is no way for me to use expresso to perform
> background correction, normalization and then examine the data before
> proceeding to other downstream analyses.
> Any suggestions on how I can accomplish this without the help of expresso?

You can perform standalone background correction using the
bg.correct.* functions

You can perform normalization at the probe intensity level using the
normalize.AffyBatch.* functions

these accept and return AffyBatch instances; you can get the intensity
measures at any stage using, say, pm()

it seems you want to avoid the summarization to an expression value to
"examine the data"; expresso
expressly wants to do a summarization to an expression value, so don't
use it, but use the components
separately.

> Thanks,
> Anjan
>
> On Wed, Oct 6, 2010 at 10:32 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>>
>> 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
>> > ===================================
>> >
>
>
>
> --
> ===================================
> anjan purkayastha, phd.
> research associate
> fas center for systems biology,
> harvard university
> 52 oxford street
> cambridge ma 02138
> phone-703.740.6939
> ===================================
>