[BioC] Can any one please help me regadrding Illumina humanv3.microarray

[Pradeep Battula]

Dear Steve,

Sorry, I am referring to this part which was there in GOstats documentation, for data(ALL)

2.1 Non-specic ltering
First we load the ALL data object and extract the subset of the data we wish to analyze:
subjects with either no cytogenetic abnormality (\NEG") or those with "ALL1/AF4".
> data(ALL, package = "ALL")
> subsetType <- "ALL1/AF4"
> Bcell <- grep("^B", as.character(ALL$BT))
> bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG", subsetType))
> bcrAblOrNeg <- ALL[, intersect(Bcell, bcrAblOrNegIdx)]
> bcrAblOrNeg$mol.biol = factor(bcrAblOrNeg$mol.biol)
We begin our non-specic ltering by removing probe sets that have no Entrez Gene iden-
tier in our annotation data.
> entrezIds <- mget(featureNames(bcrAblOrNeg), envir = hgu95av2ENTREZID)
> haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) !is.na(x))]
> numNoEntrezId <- length(featureNames(bcrAblOrNeg)) - length(haveEntrezId)
> bcrAblOrNeg <- bcrAblOrNeg[haveEntrezId, ]

Could you please tell me how to follow here for my data.,.....Thanks in advance.

----- Original Message -----
From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
Date: Monday, November 8, 2010 6:55 pm
Subject: Re: [BioC] Can any one please help me regadrding Illumina humanv3.microarray
To: Pradeep Battula <prabat at utu.fi>
Cc: bioconductor at stat.math.ethz.ch


> Hi Pradeep,
> 
> (Please keep all correspondence on list by using "reply-all" when
> replying to bioc-help messages)
> 
> On Mon, Nov 8, 2010 at 11:38 AM, Pradeep Battula <prabat at utu.fi> wrote:
> > Dear Steve,
> >
> > Thanks a lot for your suggestion. and I also want to know, whether I 
> have to perform all those Non-specific filtering tests, for the gene 
> universe....Thanks in advance.
> 
> I'm sorry, I don't follow ... what non-specific filtering tests to the
> gene universe are you referring to?
> 
> -steve
> 
> >
> > Regards,
> > Pradee.
> >
> > ----- Original Message -----
> > From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
> > Date: Monday, November 8, 2010 5:55 pm
> > Subject: Re: [BioC] Can any one please help me regadrding Illumina humanv3.microarray
> > To: Pradeep Battula <prabat at utu.fi>
> > Cc: bioconductor at stat.math.ethz.ch
> >
> >
> >> Hi,
> >>
> >> On Mon, Nov 8, 2010 at 10:44 AM, Pradeep Battula <prabat at utu.fi> wrote:
> >> > Dear All,
> >> >
> >> > I want to write a function that performs hypergeometric test for
> >> over representation against GO and KEGG, for the available example 
> of
> >> data of
> >> > background.Datat: Entrez identifiers of all probes present on
> >> Illumina human HT12 v3. microarray
> >> > DEgenes.Data: Differentially expressed genes in a real study carried
> >> out on Illumina HT12 v3. microarray
> >> >
> >> > But, the relevant documentation provided in "GOstats" and "topGO"
> >> are explained using a microarray data set  from a clinical trial in
> >> acute lymphoblastic leukemia (ALL).
> >> >
> >> > Now I want to know, can I apply the same documentation to my
> >> available data or there any minor changes I have to make.
> >>
> >> If both your background.Data and DEgenes.Data are simply vectors of
> >> entrez id's, then this is pretty straightforward. With GOstats, you
> >> can do:
> >>
> >> R>   params <- new("GOHyperGParams", geneIds=DEgenes.data,
> >>                 universeGeneIds=background.Data, annotation='org.Hs.eg.db',
> >>                 ontology='BP', ...)
> >> R> go.bp <- hyperGTest(params)
> >>
> >> -steve
> >>
> >> --
> >> Steve Lianoglou
> >> Graduate Student: Computational Systems Biology
> >>  | Memorial Sloan-Kettering Cancer Center
> >>  | Weill Medical College of Cornell University
> >> Contact Info: http://cbio.mskcc.org/~lianos/contact
> >
> 
> 
> 
> -- 
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact