[BioC] Most stable gene pairs in array experiment
Naomi Altman
naomi at stat.psu.edu
Mon Oct 19 21:44:54 CEST 2009
It sounds to me like you are looking for var(geneA-geneB).
--Naomi
At 05:54 AM 10/19/2009, anna freni sterrantino wrote:
>Hi David,
>not sure what do you mean with stable,
>but you might be interested in correlation,
>
>a=matrix(sample(1:100),4,5)
>rownames(a)=paste("gene", letters[1:4])
>colnames(a)=paste("cond", letters[1:5])
> >a
>cond a cond b cond c cond d cond e
>gene a 95 31 3 9 93
>gene b 16 67 83 81 86
>gene c 59 79 44 77 39
>gene d 36 92 41 57 66
> > cor(t(a))
> gene a gene b gene c gene d
>gene a 1.0000000 -0.5362894 -0.3830295 -0.1109239
>gene b -0.5362894 1.0000000 -0.1710537 0.3790986
>gene c -0.3830295 -0.1710537 1.0000000 0.4612277
>gene d -0.1109239 0.3790986 0.4612277 1.0000000
>
>and then across all the pairs the most correlated will be those
>that have a correlation value that is close to |1|.
>The correlation tells you how much close are two variables in terms
>of linear relationship.
>
>Hope this helps.
>Cheers
>
>A
>
>
>
>Anna Freni Sterrantino
>Ph.D Student
>Department of Statistics
>University of Bologna, Italy
>via Belle Arti 41, 40124 BO.
>
>
>
>
>________________________________
>Da: David martin <vilanew at gmail.com>
>A: bioconductor at stat.math.ethz.ch
>Inviato: Lun 19 ottobre 2009, 10:37:08
>Oggetto: [BioC] Most stable gene pairs in array experiment
>
>Hi,
>I have the following matrix with normalized log2 values:
>CondA CondB CondC CondD CondE
>geneA -6.19 -5.74 -5.82 -5 -5.59
>geneB -6.33 -5.32 -5.6 -4.88 -5.39
>geneC -6.15 -6.07 -5.6 -4.88 -5.9
>geneD -6.57 -6.11 -6.36 -5.36 -5.96
>geneD -6.74 -6.2 -5.49 -5.35 -5.95
>geneE -6.75 -6.24 -5.73 -5.63 -6.02
>
>
>Created as follows:
>geneA<-c(-6.19, -5.74, -5.82, -5, -5.59)
>geneB<-c(-6.33, -5.32, -5.6, -4.88, -5.39)
>geneC<-c(-6.15, -6.07, -5.6, -4.88, -5.9)
>geneD<-c(-6.57, -6.11, -6.36, -5.36, -5.96)
>geneD<-c(-6.74, -6.2, -5.49, -5.35, -5.95)
>geneE<-c(-6.75, -6.24, -5.73, -5.63, -6.02)
>
>mygenes<-rbind(geneA, geneB, geneC, geneD, geneE)
>colnames(mygenes)<-c("CondA", "CondB", "CondC", "CondD",
>"CondE")
>
>I'm looking for most stable pair genes across conditions. I'm not
>looking for individual gene variance but really for most stable pairs ratios.
>For e.g What is the variance of geneA vs geneB across all
>conditions. What is the most stable pair ?
>
>Any help would be appreciated.
>
>david
>
>_______________________________________________
>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
>
>
>
>
> [[alternative HTML version deleted]]
>
>_______________________________________________
>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
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
More information about the Bioconductor
mailing list