[BioC] [LIMMA] change in normexp function between limma 2.2.0 to limma 2.4.4

Gordon K Smyth smyth at wehi.EDU.AU
Wed Dec 14 12:57:39 CET 2005


Dear Ron,

If you type changeLog(n=100) in limma 2.4.4, you'll see that I made a couple of changes to normexp
in limma 2.3.1 which apparently have not been very successful.

Someone else asked the same question as you have a couple of weeks ago, see
https://www.stat.math.ethz.ch/pipermail/bioconductor/2005-December/011125.html

Best wishes
Gordon

> Date: Wed, 14 Dec 2005 09:43:25 +0200
> From: "Ron Ophir" <ron.ophir at weizmann.ac.il>
> Subject: [BioC] [LIMMA] change in normexp function between limma 2.2.0
> 	to	limma 2.4.4
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <s39fe957.014 at wisemail.weizmann.ac.il>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
> We have a microarray experiment of cDNA of 36 spotted arrays, reference
> design.
> Two persons run the analysis with same code and the same data for
> education purposes. One loaded limma package version
>>sessionInfo()
> R version 2.2.0, 2005-10-06, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"
>
> other attached packages:
>   limma
> "2.4.4"
> and the other
>>sessionInfo()
> R version 2.2.0, 2005-10-06, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"
>
> other attached packages:
>   limma
> "2.2.0"
>
> we run the following code:
>
> targets<-readTargets()
> raw <-
> read.images(targets=targets,format="genepix",wt.fun=wtflags(0.1))
> #genepix format
> raw$genes<-readMyGAL()
> png(file="densityPlotPreNormalized.png",width=800,height=400)
> plotDensities(raw)
> dev.off()
>
> RGb<-backgroundCorrect(raw, method="normexp", offset=50)
>
> png(file="densityPlotPreNormalizedBS.png",width=800,height=400)
> plotDensities(RGb)
> dev.off()
>
> data<-normalizeWithinArrays(RGb) # with background substraction
>
> png(file="densityPlotNormalized.png",width=800,height=400)
> plotDensities(data)
> dev.off()
>
>> max(raw$R)
> [1] 63762
>> max(raw$G)
> [1] 64016
>
> for limma 2.4.4
>> max(RGb$R)
> [1] 6.50953e+272
>> max(RGb$G)
> [1] 3.146027e+248
>
> for limma 2.2
>
>> max(RGb_all$R)
> [1] 63446.46
>> max(RGb_all$G)
> [1] 63820.55
>
> Where do you the problem might be?
>
> Thanks,
> Ron
>
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: densityPlotPreNormalized.png
> Type: image/png
> Size: 5985 bytes
> Desc: not available
> Url :
> https://stat.ethz.ch/pipermail/bioconductor/attachments/20051214/66658510/densityPlotPreNormalized-0001.png
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: densityPlotPreNormalizedBS2.4.png
> Type: image/png
> Size: 3008 bytes
> Desc: not available
> Url :
> https://stat.ethz.ch/pipermail/bioconductor/attachments/20051214/66658510/densityPlotPreNormalizedBS2.4-0001.png
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: densityPlotPreNormalizedBS2.2.png
> Type: image/png
> Size: 5979 bytes
> Desc: not available
> Url :
> https://stat.ethz.ch/pipermail/bioconductor/attachments/20051214/66658510/densityPlotPreNormalizedBS2.2-0001.png



More information about the Bioconductor mailing list