[BioC] Variance

[David martin]

Thanks,
It's working.
To get he min value i run
min = which.min(myvars)
However, how do I know the calculated variance ?? as which.min returns 
the index but not the variance.

thanks


john seers (IFR) wrote:
> Hi
> 
> Something like this?
> 
>     
> 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")
> 
> myvars<-apply(mygenes, 1, var)
> 
> myvars[which(min(myvars) == myvars)]
> 
> 
> #  geneA 
> #0.18827
> 
> Note that this needs a matrix so you will need to convert your dataframe
> to work. (See ?data.matrix). Also I think using the min command will not
> always work to index the myvars, but it shows the idea.
> 
> See ?plot for plotting.
> 
> Regards
> 
> J
> 
> 
> 
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of David
> martin
> Sent: 22 June 2009 13:56
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Variance
> 
> Hello,
> I'm newbie with R.
> I have a dataframe as follows. The microarray data has been normalized 
> using spike in controls and the values shown are 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
> 
>  From this small subset (in fact i have a larger dataframe) i would like
> 
> to know which gene has the lowest variance. I would like to see is some 
> of these genes could be used as reference genes for RT-PCr experiments.
> How can i plot and get the variance from this genes and see what would 
> the best candidates to be used as reference genes.
> 
> thanks,
> 
> david
> 
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