A quick question and hopefully a quick answer in reply.... I have data from Agilent bovine chips. Are the spike-in probe replicates (of which there are 32 on each chip) supposed to be highly replicable on an MA plot? Some of my chips show good reproducibility of the spike- in's on MA plots, but others show streaks running bottom left to top right on the MA plot. I'm wondering if this may indicate problems with some of the chips!? Find my code below. Cheers, Nath My SpotTypes.txt file is like: <spottypes.txt> SpotType ControlType ProbeName col Other * * white Probe 0 * black Negative -1 *3xSLv1* blue E1A 1 1 *E1A_r60_1$ red E1A n11 1 *E1A_r60_n11$ pink E1A a20 1 *E1A_r60_a20$ brown E1A 3 1 *E1A_r60_3$ orange E1A a104 1 *E1A_r60_a104$ yellow E1A a107 1 *E1A_r60_a107$ green E1A a135 1 *E1A_r60_a135$ blueviolet E1A a22 1 *E1A_r60_a22$ cyan E1A a97 1 *E1A_r60_a97$ bisque4 E1A n9 1 *E1A_r60_n9$ aquamarine </spottypes.txt> RG <- read.maimages(files=targets$FileName, source="agilent", names=targets$Name, ) spottypes <- readSpotTypes() RG$genes$Status <- controlStatus(spottypes, RG) nArrays <- ncol(RG) png(file = "Raw_MA.png", type = "cairo1", width=5*ceiling(sqrt(nArrays)), height=5*ceiling(sqrt(nArrays)), units="in", res=300) par(mfrow=c(ceiling(sqrt(nArrays)), ceiling(sqrt(nArrays))), mar=c(5.1,4.1,3,1)) for(i in 1:nArrays) { plotMA(RG, array=i, pch=16) } dev.off()

I am not familiar with this chip, but we did find that the controls on our custom Agilent chips had striking dye bias. However, the bias was similar on every chip. I usually do a scatterplot matrix of every channel against all other channels with the same treatment. (logarithmic scale) Even without normalization, these should be diagonal, although there is usually some curvature. If they are highly scattered, you might have a problem. We found that the labeling dyes can degrade rapidly under some conditions. --Naomi At 06:25 AM 5/7/2009, Nathan S. Watson-Haigh wrote: >A quick question and hopefully a quick answer in reply.... > >I have data from Agilent bovine chips. Are the spike-in probe replicates >(of which there are 32 on each chip) supposed to be highly replicable on >an MA plot? Some of my chips show good reproducibility of the spike- in's >on MA plots, but others show streaks running bottom left to top right on >the MA plot. I'm wondering if this may indicate problems with some of >the chips!? > >Find my code below. > >Cheers, >Nath > > >My SpotTypes.txt file is like: > ><spottypes.txt> >SpotType ControlType ProbeName col >Other * * white >Probe 0 * black >Negative -1 *3xSLv1* blue >E1A 1 1 *E1A_r60_1$ red >E1A n11 1 *E1A_r60_n11$ pink >E1A a20 1 *E1A_r60_a20$ brown >E1A 3 1 *E1A_r60_3$ orange >E1A a104 1 *E1A_r60_a104$ yellow >E1A a107 1 *E1A_r60_a107$ green >E1A a135 1 *E1A_r60_a135$ blueviolet >E1A a22 1 *E1A_r60_a22$ cyan >E1A a97 1 *E1A_r60_a97$ bisque4 >E1A n9 1 *E1A_r60_n9$ aquamarine ></spottypes.txt> > > >RG <- read.maimages(files=targets$FileName, source="agilent", >names=targets$Name, ) >spottypes <- readSpotTypes() >RG$genes$Status <- controlStatus(spottypes, RG) > >nArrays <- ncol(RG) >png(file = "Raw_MA.png", type = "cairo1", >width=5*ceiling(sqrt(nArrays)), height=5*ceiling(sqrt(nArrays)), >units="in", res=300) >par(mfrow=c(ceiling(sqrt(nArrays)), ceiling(sqrt(nArrays))), >mar=c(5.1,4.1,3,1)) >for(i in 1:nArrays) { > plotMA(RG, array=i, pch=16) >} >dev.off() > > >_______________________________________________ >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