
I was wondering how to extract feature importance contributing to a given classifier.
e.g. class_lda <- classification(X = khanX, y=khanY, learningsets = fiveCV5iter, classifier = ldaCMA, genesel= genesel_da, nbgene = 10)
I would like to get a list of features (probesets) and associated importance contributing to class_lda (Some will have 0 importance??).
Is there a way to do this? 
Thanks in advance.
So.

> Date: Sat, 21 Jul 2012 22:22:54 -0500
> From: xiaskyer@gmail.com
> To: jmacdon@uw.edu
> CC: maintainer@bioconductor.org; bioconductor@r-project.org
> Subject: Re: [BioC]	GOstats: get genes for correspondā ing enriched GO term
> 
> Hi, Jim
> Sorry for not including enough information.
> What I have done is simple:
> 
> Firs, I used most of yeast genome (ORF gene id) as  universeGeneIds
> like:
> YAL001C
> YAL002W
> YAL003W
> YAL004W
> YAL005C
> YAL007C
> YAL008W
> YAL009W
> ...
> (size  5616)
> 
> 
> then I used a shorter list of genes as geneIds like:
> YAL022C
> YAL023C
> YAL024C
> YAL025C
> YAL026C
> YAL027W
> YAL028W
> YAL029C
> ...
> (size 500)
> 
> then I performed the test.  (I think I did reasonably because GOstats can
> perform test on geneid instead of probesetid, as they describe "If you are
> using the YEAST annotation package, the vector will consist of yeast
> systematic names.")
> 
> then I got result :
> Gene to GO BP test for over-representation
> 1660 GO BP ids tested (9 have p< 0.01)
> Selected gene set size: 427
> Gene universe size: 5616
> Annotation package: org.Sc.sgd
> What I need to next is to try get which geneids (represnted in ORF yeast
> systematic names ) contribute to which enriched GO term (p<0.01).
> I don't guess that it should necessarily be in probesetid since all inputs
> are in ORF/ yeast systematic names and not from any microarray data.
> 
> 
> Many thanks for your help,
> 
> Tian
> 
> 
> 
> 
> 
> On Sat, Jul 21, 2012 at 9:37 PM, James W. MacDonald <jmacdon@uw.edu> wrote:
> 
> >
> >
> > On 7/21/2012 9:43 PM, Lan Sky wrote:
> >
> >> Hi, Jim
> >> Thanks for your information.
> >> I actually don't have any probesetID.
> >> I only used yeast ORF id to perform the GO.
> >> Do I need to do some mapping from ORF to probeset?
> >> In the message I got, it says, "If you want to know theprobesets that
> >> contributed to this result
> >> either usea named vector for geneIds, or pass a vector of probeset IDs
> >> via sigProbesets."
> >> "either use a named vector for geneIds."
> >> what is that supposed to be the input?
> >>
> >> Dose it mean geneId instead of probeset?
> >>
> >
> > It depends on how you did things. You have been pretty cryptic about what
> > you have done, so we have to read between the lines. In general, people use
> > microarray data to do GO analyses. In which case the genes are interrogated
> > by one or more 'reporter' molecules, which if the manufacturer is
> > Affymetrix, are called probesets.
> >
> > When you have a significant GO term, one might want to know which of the
> > significant reporter molecules contributed to that result. So in the case
> > of an Affy analysis, you would pass in a vector of probeset IDs. So if you
> > don't have Affy data, then I assume you have some other manufacturer IDs
> > you could use. Perhaps you could feed in gene IDs, but that wasn't the
> > original intent, and may not work.
> >
> > Best,
> >
> > Jim
> >
> >
> >  Thanks,
> >> Tim
> >>
> >> On Sat, Jul 21, 2012 at 1:16 PM, James W. MacDonald <jmacdon@uw.edu<mailto:
> >> jmacdon@uw.edu>> wrote:
> >>
> >>     Hi Tim,
> >>
> >>
> >>     On 7/21/2012 10:25 AM, Lan Sky wrote:
> >>
> >>         Hi, Yuan
> >>         Thanks alot for your help.
> >>         I used yeast ORF id as input vectors of geneIds and
> >>         universeGeneIds.
> >>         These are the summary of GOHyperGResult instance
> >>
> >>         Gene to GO BP  test for over-representation
> >>         1660 GO BP ids tested (9 have p<  0.01)
> >>         Selected gene set size: 427
> >>              Gene universe size: 5616
> >>              Annotation package: org.Sc.sgd
> >>
> >>         when I used
> >>
> >>         ps<-probeSetSummary(over,0.05)
> >>
> >>         I got warning:
> >>         The vector of geneIds used to create the GOHyperGParamsobject
> >>         was not a
> >>         named vector.
> >>         If you want to know theprobesets that contributed to this result
> >>         either usea named vector for geneIds, or pass a vector of
> >>         probeset IDs
> >>         via sigProbesets.
> >>         when I use the input geneIDs (segene) to pass the vector via
> >>         sgProbesets
> >>         like:
> >>
> >>         ps<-probeSetSummary(over,0.05,**,segene)  //segene is input
> >>         yeast ORF ID
> >>
> >>         I still got a empty resut.
> >>         Did I do something wrong?
> >>
> >>
> >>     Well if you actually used the code above, I am surprised it even
> >>     ran. Double commas usually result in an error.
> >>
> >>     Also, please re-read the message you got from probeSetSummary().
> >>     You are supposed to be passing in a vector of probeset IDs, not
> >>     re-sending the ORF IDs.
> >>
> >>     Best,
> >>
> >>     Jim
> >>
> >>
> >>
> >>         Thanks for further help.
> >>
> >>         Tim
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>         On Sat, Jul 21, 2012 at 3:01 AM, Yuan Hao<yuan.x.hao@gmail.com
> >>         <mailto:yuan.x.hao@gmail.com>>  wrote:
> >>
> >>
> >>             Would "probeSetSummary()" do what your want?
> >>
> >>             Yuan
> >>
> >>
> >>             On 21 Jul 2012, at 02:47, Tim [guest] wrote:
> >>
> >>
> >>                 Hi,
> >>
> >>                 I used GOstats to perform enrichment test on a set of
> >>                 genes (20).
> >>
> >>                 There are 7 GO terms with pvalue less than cuttoff and
> >>                 therefore shown in
> >>                 the result table.
> >>
> >>                 How can I get the information that which gene in the
> >>                 input gene set
> >>                 belong to which GO term of these enriched GO terms?
> >>
> >>
> >>
> >>
> >>                 best,
> >>
> >>                 Tim
> >>
> >>                 -- output of sessionInfo():
> >>                 Thanks for any comments.
> >>
> >>                 --
> >>                 Sent via the guest posting facility at
> >>                 bioconductor.org <http://bioconductor.org>.
> >>
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> > Biostatistician
> > University of Washington
> > Environmental and Occupational Health Sciences
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> >
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