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 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/

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@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@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@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@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+