[BioC] VennDiagram quesiont in limma

[Jianping Jin]

Dear Jenny and Gordon:

Many thanks to you for your help. All you recommended work well for me.

cheers!

Jianping

--On Thursday, June 01, 2006 9:52 AM -0500 Jenny Drnevich 
<drnevich at uiuc.edu> wrote:

> Hi Jianping,
>
> I recently wrote a detailed response along these same lines for a client.
> It's not as elegant as Gordon's solution, but it works for me and can be
> modified for any combination you want:
>
> The coded.results object (output from 'decideTests') has the matrix of
> -1, 0 , and 1s. If BvT and AvT are the 5th and 6th columns in the
> coded.results object, you can do:
>
> BsameAup <- which(coded.results[,5] == 1 & coded.results[,6] == 1)
>
> This will give you a vector of row numbers you can use to subset most
> other objects that have the genes in the same order:
>
> BsameAupgenes <- fit$genes[BsameAup,]  #remember that between [], to the
> left of the , refers to rows and to the right refers to columns
>
> You can actually combine these two steps if you want to get fancy:
>
> BsameAdowngenes <- fit$genes[coded.results[,5] == -1 & coded.results[,6]
> == -1 , ]
>
> This subsetting uses TRUE/FALSE output (a conditional statement), such as
> == (equal to), != (not equal to), >, <=, etc.
>
> BupAdown <- which(coded.results[,5] == 1,& coded.results[,6] != 1)
> BchangedAnot <- which(coded.results[,5] != 0 & coded.results[,6] == 0)
>
> In case you want to use it, the "or" equivalent of "&" is "||" (two
> straight characters, not the letter l or capital I; on my keyboard it is
> on the same key as the backslash \). You can also put more than two
> conditional statements together - just tack as many as you want using &
> or ||.
>
> Cheers,
> Jenny
>
>
> At 09:23 AM 6/1/2006, jjin at email.unc.edu wrote:
>> Hi Gordon,
>>
>> Thanks very much for your help! That is what I wanted to extract. But
>> what if I wanted genes DE for "A" and "B" but "C"? Or just for "A", not
>> "B" and "C"?
>>
>> best wishes!
>>
>> Jianping
>>
>>
>> Quoting Gordon Smyth <smyth at wehi.EDU.AU>:
>>
>> > Dear Jianping,
>> >
>> > I may be mis-interpreting your question (I'm not sure what you mean
>> > by a "session"), but I think you just want the gene lists
>> > corresponding to the counts in the Venn diagram.
>> >
>> > Suppose you have a fitted model 'fit' with columns "A", "B" and "C".
>> > Then
>> >
>> >   vennDiagram(fit)
>> >
>> > will give you a Venn diagram with 8 counts in it. You can do the
>> > diagram in two steps
>> >
>> >   results <- decideTests(fit)
>> >   vennDiagram(results)
>> >
>> > and this allows you to extract the gene lists. Suppose you want the
>> > genes DE for both "A" and "B", you could use
>> >
>> >   myGenes <- apply(results[,c("A","B")],1,all)
>> >   fit$genes[myGenes,]
>> >
>> > to see the gene list.
>> >
>> > Best wishes
>> > Gordon
>> >
>> >> Date: Tue, 30 May 2006 13:22:08 -0400
>> >> From: Jianping Jin <jjin at email.unc.edu>
>> >> Subject: [BioC] VennDiagram quesiont in limma
>> >> To: BioConductor_list <bioconductor at stat.math.ethz.ch>
>> >> Message-ID: <DBCD9D517C98493F3A37FA9D at unc-jpjin.pmbb.med.unc.edu>
>> >> Content-Type: text/plain; charset=us-ascii; format=flowed
>> >>
>> >> Dear list:
>> >>
>> >> I am wondering if there is an easy way or a function by which one can
>> >> extract (list) any session of genes, either in common or not in
>> >> common
>> with
>> >> other sesseion(s), in vennDiagram of limma? I assumed that vennDiagram
>> >> should be able to allow to do that. But I did not find anything like
>> >> that after reading the on-line instructions.
>> >>
>> >> Many thanks if you could help me out!
>> >>
>> >> Jianping
>> >>
>> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> >> x Jianping Jin Ph.D.            x
>> >> x Bioinformatics scientist      x
>> >> x Center for bioinformatics     x
>> >> x 3133 Bioinformatics Building  x
>> >> x CB# 7104                      x
>> >> x University of North Carolina  x
>> >> x Chapel Hill, NC 27599         x
>> >> x Tel: (919)843-6105            x
>> >> x Fax: (919)843-3103            x
>> >> x E-mail: jjin at email.unc.edu    x
>> >> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> >
>> >
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu



xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
x CB# 7104                      x
x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
x Fax: (919)843-3103            x
x E-mail: jjin at email.unc.edu    x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx