[BioC] Difference between GO2ALLPROBES and GO2PROBE ?

[James W. MacDonald]

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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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109