[BioC] Error in normalisation routines

[Robert Gentleman]

On Feb 21, 2005, at 1:55 AM, Dion Whitehead wrote:

> Hi all,
>
> I am getting this frustrating error in the 'affy' package, using the  
> 'justMAS' function.  I have looked at the function but cannot figure  
> out where the error comes from of how to fix it.
>
> x <- justMAS(cold.root.00.5.raw, tgt=100)
>
> Background correcting
> Retrieving data from AffyBatch...done.
> Computing expression calls...
> ....done.
> scaling to a TGT of 100 ...Scale factor for: COLD_30MIN_ROOT_REP1.cel  
> 0.337464082097439
> Scale factor for: COLD_30MIN_ROOT_REP2.cel 0.402367050097728
> Scale factor for: CONTROL_30MIN_ROOT_REP1.cel 0.342672641420889
> Scale factor for: CONTROL_30MIN_ROOT_REP2.cel 0.341954877809006
> Error in sigToEnv(signature, fdef) : Trying to get slot "signature"  
> from an object of a basic class ("NULL") with no slots
>

As to the exact nature - no, but as to some general strategies:

1) please tell us the version of R, the OS and the version of affy (we  
can't really help without some pretty basic information) - there are  
posting guidelines for R help, and they apply here as well

2) at this point using traceback() will pinpoint the location of the  
error, and may help someone
identify the real problem

3) an alternative is to set
  options(error=recover)
  and to enter the interactive debugger at that point - then you can try  
to figure out what is
going wrong and where.

4) there is a fair amount of information on debugging R available -  
reading it is often worthwhile

  Robert


> Anyone have any ideas?
>
> Dion
>
> -- ***************************
> Dion Whitehead
> Division of Bioinformatics
> The Westfalian Wilhelms University of Muenster
> Botanical Institute, Schlossplatz 4
> D48149 Muenster
> Germany
>
> Phone: +49-251-83-21633
> Fax:   +49-251-83-21631
> http://www.uni-muenster.de/Biologie.Botanik/ebb/
>
> _______________________________________________
> Bioconductor mailing list
> 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                                              
                          |
+----------------------------------------------------------------------- 
----------------+


+----------------------------------------------------------------------- 
----------------+
| 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                                              
                          |
+----------------------------------------------------------------------- 
----------------+


+----------------------------------------------------------------------- 
----------------+
| 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                                              
                          |
+----------------------------------------------------------------------- 
----------------+