Hi Marco,
Thanks...
That happens.
I wanted to include one more condition on the top.table list of logFC to
consider only those which are greater than or equal to1 and less than or
equal to -1.
I just tried to expand the code

> your.results1<-your.results[your.results$logFC < -1,]
> your.results2<-your.results1[your.results1$logFC > 1,]
> write.table(your.results2,"Panc1_final_list.txt",sep='\t')

but just got a blank txt file with headings.I also tried using & and |
operators, but got errors.
I hope you could help on this.
Thanks,
Viritha


On Tue, Feb 8, 2011 at 3:32 PM, Manca Marco (PATH) <
m.manca@maastrichtuniversity.nl> wrote:

> Sorry, I had overlooked that part of the question... I thought you just
> wanted help in setting the threshold so I just added that line to your code.
>
> As James has already mentioned to have the full list of genes in your
> results you have to set something like:
>
>  design <- model.matrix(~factor(rep(1:2, each=3)))
>  fit <- lmFit(eset, design)
>  fit2 <- eBayes(fit)
> # If you want the first 10000 results... but usually I put
> "number=THE_NUMBER_OF_GENES_ON_MY_CHIP"
> top.list<-topTable(fit2,number=10000,coef=2,adjust="BH")
> your.results <- top.list[top.list$adj.P.Val < 0.05, ]
>
> ...I can only say to my defense "you only see what you look for" =P I
> should have given a more complete answer since the beginning.
>
> All the best, Marco
>
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology
> - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX
> Maastricht
>
> E-mail: m.manca@maastrichtuniversity.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
>
> *********************************************************************************************************************
>
> This email and any files transmitted with it are confidential and solely
> for the use of the intended recipient.
>
> It may contain material protected by privacy or attorney-client privilege.
> If you are not the intended recipient or the person responsible for
>
> delivering to the intended recipient, be advised that you have received
> this email in error and that any use is STRICTLY PROHIBITED.
>
> If you have received this email in error please notify us by telephone on
> +31626441205 Dr Marco MANCA
>
>
> *********************************************************************************************************************
> ________________________________________
> Da: viritha kaza [viritha.k@gmail.com]
> Inviato: martedė 8 febbraio 2011 19.01
> A: Manca Marco (PATH)
> Cc: bioconductor@stat.math.ethz.ch
> Oggetto: Re: [BioC] Time course experiment....
>
> Hi Marco,
> Thanks for your reply.
> But topTable by default only gives top 10.So how do I know the number in
> topTable fuction which satisfies the criteria of 0.05 that I need to give.
> waiting for your reply...
> Thanks,
> Viritha
>
> On Tue, Feb 8, 2011 at 12:35 PM, Manca Marco (PATH) <
> m.manca@maastrichtuniversity.nl<mailto:m.manca@maastrichtuniversity.nl>>
> wrote:
> Hi Viritha,
>
> just do
>
> code:
>  design <- model.matrix(~factor(rep(1:2, each=3)))
>  fit <- lmFit(eset, design)
>  fit2 <- eBayes(fit)
> top.list<-topTable(fit2,coef=2,adjust="BH")
> your.results <- top.list[top.list$adj.P.Val < 0.05, ]
>
> ...it should do the trick...
>
> All the best, Marco
>
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: Experimental Vascular Pathology group, Dept of Pathology
> - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX
> Maastricht
>
> E-mail: m.manca@maastrichtuniversity.nl<mailto:
> m.manca@maastrichtuniversity.nl>
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
>
> *********************************************************************************************************************
>
> This email and any files transmitted with it are confidential and solely
> for the use of the intended recipient.
>
> It may contain material protected by privacy or attorney-client privilege.
> If you are not the intended recipient or the person responsible for
>
> delivering to the intended recipient, be advised that you have received
> this email in error and that any use is STRICTLY PROHIBITED.
>
> If you have received this email in error please notify us by telephone on
> +31626441205 Dr Marco MANCA
>
>
> *********************************************************************************************************************
> ________________________________________
> Da: bioconductor-bounces@r-project.org<mailto:
> bioconductor-bounces@r-project.org> [bioconductor-bounces@r-project.org
> <mailto:bioconductor-bounces@r-project.org>] per conto di viritha [
> viritha.k@gmail.com<mailto:viritha.k@gmail.com>]
> Inviato: martedė 8 febbraio 2011 18.14
> A: bioconductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch>
>  Oggetto: Re: [BioC] Time course experiment....
>
> Naomi Altman <naomi@...> writes:
>
> >
> > I did not get the original posting, but doesn't Sohail just need
> > "TopTable" for this?
> >
> > --Naomi
>
> Hi Naomi,
> I had a similiar issue and used TopTable but I am getting only first 10 but
> how
> should I write the code to get selected probesets based on an adjusted
> p-value
> less than or equal to 0.05.
>
> code:
>  design <- model.matrix(~factor(rep(1:2, each=3)))
>  fit <- lmFit(eset, design)
>  fit2 <- eBayes(fit)
> topTable(fit2,coef=2,adjust="BH")
>
> I have 3 control and 3 treated samples.The eset has the probenames and the
> expression matrix.
> So my question is how do I get the data of all the probesets which pass
> this
> criteria?
> Thanks,
> Viritha
>
> >
> > At 08:51 AM 1/2/2006, Gordon Smyth wrote:
> > >Dear Sohail,
> > >
> > >Well, there are lots of ways to generate such a table. Perhaps the
> simplest
> is
> > >
> > >    fitsel <- fit2[sel.dif, ]
> > >    as.data.frame( fitsel )
> > >
> > >Best wishes
> > >Gordon
> > >
> > > >Date: Tue, 20 Dec 2005 14:03:43 -0500
> > > >From: "Khan, Sohail" <khan@...>
> > > >Subject: [BioC] Time course experiment....
> > > >To: <bioconductor@...>
> > > >
> > > >Dear List,
> > > >
> > > >I have performed a time course analysis using limma, as described in
> > > >"Bioinformatics and Computational Biology Solutions ........".
> > > >How can I get a list of differentially expressed genes?  I've tried
> > > >the code below:
> > > >sel.dif<-p.adjust(fit2$F.p.vlaue,method="fdr") <0.05
> > > >This produces a logical vector, right?.  I would like a table of
> > > >differentially expressed genes with p vales etc.  Sorry, if I missed
> > > >this in the limma user's guide.  Thanks for any suggestions.
> > > >
> > > >
> > > >Sohail Khan
> > > >Scientific Programmer
> > > >COLD SPRING HARBOR LABORATORY
> > > >Genome Research Center
> > > >500 Sunnyside Boulevard
> > > >Woodbury, NY 11797
> > > >(516)422-4076
> > >
> > >_______________________________________________
> > >Bioconductor mailing list
> > >Bioconductor@...
> > >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
> > Naomi S. Altman                                814-865-3791 (voice)
> > Associate Professor
> > Dept. of Statistics                              814-863-7114 (fax)
> > Penn State University                         814-865-1348 (Statistics)
> > University Park, PA 16802-2111
> >
>
> _______________________________________________
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