[BioC] Problem with Expresso and RMA

[Robert Gentleman]

which R? it needs to be R 2.0.1 (or there abouts and not the 2.1.0  
candidate)
<more comments below>
On Feb 15, 2005, at 10:14 AM, McGee, Monnie wrote:

> I am sorry.  I know better than to leave out such important  
> information.
>
> I am using R on a Macintosh Powerbook G4.  I was using R through an  
> X-windows interface (XFree86 4.3.0).  The version of affy I am running  
> is 1.5.8 and the Biobase version is 1.5.0.
>
> ________________________________
>
> From: Vincent Carey 525-2265 [mailto:stvjc at channing.harvard.edu]
> Sent: Tue 2/15/2005 9:33 AM
> To: McGee, Monnie
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Problem with Expresso and RMA
>
>
>
> To help you diagnose this we will need to know what version of R
> you are running, and what versions of affy and Biobase you have
>
> packageDescription("affy")$Version
>
> it would also be nice if you told us what platform you are using
>
>> Dear BioC Users,
>>
>> I am analyzing data from an AffyBatch object (that I've called
>> "allarray") with the following features:
>>
>>> print(allarray)
>> AffyBatch object
>> size of arrays=1164x1164 features (63515 kb)
>> cdf=HG-U133_Plus_2 (54675 affyids)
>> number of samples=6
>> number of genes=54675
>> annotation=hgu133plus2
>>
>> Note that there are no replicates in this array.  In other words, the  
>> 6
>> samples are 6 different arrays with 6 different RNA treatments.  I'm
>> trying to understand which genes are differentially expressed among  
>> the
>> 6 arrays.
>>
>> I wanted to use RMA normalization, so I typed rma(allarray) and
>> received the following error
>>> eset1 <- rma(allarray)
>> Background correcting
>> Normalizing
>> Calculating Expression
>> Error in sigToEnv(signature, fdef) : Trying to get slot "signature"
>> from an object of a basic class ("NULL") with no slots
>>

try traceback()
right here

something is confused about the class -
where did you get the affyBatch object and are you sure it was created  
with the same
version of affy as you are using

>> I tried to do the same thing using expresso and received the same
>> error.  Here's what I typed and the response of bioconductor:
>>> eset1
>> <-
>> expresso(allarray,bgcorrect.method="rma",normalize.method="quantiles", 
>> pm
>> correct.method="pmonly",summary.method="medianpolish")
>> background correction: rma
>> normalization: quantiles
>> PM/MM correction : pmonly
>> expression values: mas
>> background correcting...done.
>> normalizing...Error in sigToEnv(signature, fdef) : Trying to get slot
>> "signature" from an object of a basic class ("NULL") with no slots
>>
>> I read an archived message with said that it was not a good idea to  
>> use
>> median polish without replicated arrays, and that it would be better  
>> to
>> use rlm.  However, I can't seem to get an eset so that I can use rlm.
>>
>> The funny thing is, just last week, expresso was working fine.  I was
>> able to obtain an eset with no errors, using the same AffyBatch with
>> the same choices for all the methods.
>>
>> I would appreciate some help.
>>
>> Thanks,
>> Monnie
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
>
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
+----------------------------------------------------------------------- 
----------------+
| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
       |
| Fred Hutchinson Cancer Research Center                                 
          |
| email: rgentlem at fhcrc.org                                              
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