[BioC] Difference between GO2ALLPROBES and GO2PROBE ?

[Saurin Jani]

Hi Sir,

Sure, I will do so.

Thank you,
Saurin





--- "James W. MacDonald" <jmacdon at med.umich.edu>
wrote:

> Saurin Jani wrote:
> > Hi,
> > 
> > I think I have installation problem, somehow I did
> not
> > install properly or something but I am getting
> when I
> > do ?GO2PROBE
> > 
> 
> This is not surprising since there is nothing called
> GO2PROBE! I presume 
> you are interested in a particular environment in a
> particular 
> annotation package? For instance, you can see the
> help page for the 
> hgu133aGO2PROBE this way:
> 
> library(hgu133a)
> ?hgu133aGO2PROBE
> ?hgu133aGO2ALLPROBES
> 
> As Robert mentioned in his original response, there
> is a huge amount of 
> information supplied with each of the BioC packages,
> as well as with R 
> itself. All this information, as well as the
> functions themselves (not 
> to mention the help that is offered on this
> listserv), have been offered 
> to you for free.
> 
> One expectation of an open source project such as
> BioC is that people 
> who choose to use the software will make use of all
> this free 
> information *first* and ask questions on the
> listserv only as a last 
> resort (as mentioned above, the help given is
> *free*, and usually 
> uncompensated). Please do yourself (and us) a favor
> and familiarize 
> yourself with some of this information so you don't
> have to be so 
> reliant on this listserv for answers.
> 
> Best,
> 
> Jim
> 
> 
> > 
> >>?GO2PROBE
> > 
> > No documentation for 'GO2PROBE' in specified
> packages
> > and libraries:
> > you could try 'help.search("GO2PROBE")'
> > 
> > and below messages including warnings for :
> > 
> > 
> >>help.search("GO2PROBE");
> > 
> > Help files with alias or concept or title matching
> > 'GO2PROBE' using
> > fuzzy matching:
> > 
> > cleanSrcObjs(AnnBuilder)
> >                         Supporting function that
> may
> > no of any other
> >                         usese
> > hgu133aGO2PROBE(hgu133a)
> >                         Mappings between GO
> > identifiers and probe
> >                         identifiers representing
> genes
> > that are
> >                         directly associated with
> the
> > GO ids
> > hgu95av2GO2PROBE(hgu95av2)
> >                         Mappings between GO
> > identifiers and probe
> >                         identifiers representing
> genes
> > that are
> >                         directly associated with
> the
> > GO ids
> > hu6800GO2PROBE(hu6800)
> >                         Mappings between GO
> > identifiers and probe
> >                         identifiers representing
> genes
> > that are
> >                         directly associated with
> the
> > GO ids
> > moe430aGO2PROBE(moe430a)
> >                         Mappings between GO
> > identifiers and probe
> >                         identifiers representing
> genes
> > that are
> >                         directly associated with
> the
> > GO ids
> > rae230aGO2PROBE(rae230a)
> >                         Annotation of GO
> identifiers
> > by probe ids
> >                         corresponding to the GO
> ids
> > YEASTGO2PROBE(YEAST)    Mappings between GO
> > identifiers and probe
> >                         identifiers representing
> genes
> > that are
> >                         directly associated with
> the
> > GO ids
> > 
> > 
> > Type 'help(FOO, package = PKG)' to inspect entry
> > 'FOO(PKG) TITLE'.
> > 
> > Warning messages:
> > 1: No Rd contents for package 'GeneTraffic' in
> > '/usr/local/lib/R/library' in:
> help.search("GO2PROBE")
> > 2: No Rd contents for package 'KEGGSOAP' in
> > '/usr/local/lib/R/library' in:
> help.search("GO2PROBE")
> > 3: No Rd contents for package 'R2HTML' in
> > '/usr/local/lib/R/library' in:
> help.search("GO2PROBE")
> > 4: No Rd contents for package 'RCurl' in
> > '/usr/local/lib/R/library' in:
> help.search("GO2PROBE")
> > 5: No Rd contents for package 'SSOAP' in
> > '/usr/local/lib/R/library' in:
> help.search("GO2PROBE")
> > 
> > 
> > 
> > 
> > I have R-2.0 with develOK=TRUE version. Is
> something
> > wrong in my installation/configure process?
> > 
> > Thanks,
> > Saurin
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > --- Robert Gentleman <rgentlem at jimmy.harvard.edu>
> > wrote:
> > 
> > 
> >>On Thu, Oct 14, 2004 at 09:20:49AM -0700, Saurin
> >>Jani wrote:
> >>
> >>>Hi,
> >>>
> >>>What is difference between GO2ALLPROBES and
> >>
> >>GO2PROBE?
> >>
> >>  Hi,
> >>    All of these are well documented in the
> >>appropriate manual
> >>    pages, did you not get them or are you unable
> to
> >>find them for
> >>    some reason?  ?GO2PROBE is one way, as is
> using
> >>help.start or any
> >>    of a number of other methods. You might find
> it
> >>helpful to spend
> >>    some time reading some of the R manuals as
> well.
> >>
> >>   Robert
> >>
> >>
> >>>
>
>>unique(lookUp(DECCnodes[[1]],"moe430a","GO2PROBE"))
> >>
> >>>I get : 76 probes
> >>>
> >>>
> >>
> >
>
unique(lookUp(DECCnodes[[1]],"moe430a","GO2ALLPROBES"))
> > 
> >>>I get : 281 probes
> >>>
> >>>
> >>>Thanks,
> >>>Saurin
> >>>
> >>>_______________________________________________
> >>>Bioconductor mailing list
> >>>Bioconductor at stat.math.ethz.ch
>
>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>
> >>-- 
> >>
> > 
> >
>
+---------------------------------------------------------------------------+
> > 
> >>| Robert Gentleman                 phone : (617)
> >>632-5250                   |
> >>| Associate Professor              fax:   (617) 
> >>632-2444                   |
> >>| Department of Biostatistics      office: M1B20  
>  
> >>                       |
> >>| Harvard School of Public Health  email:
> >>rgentlem at jimmy.harvard.edu        |
> >>
> > 
> >
>
+---------------------------------------------------------------------------+
> > 
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
>