[BioC] Can not plot only one chip at the time...

[James MacDonald]

If you are just trying to tell the curves apart, you might simply give them different colors. I usually use  something like this:

hist(NHEK, type="l", lty=1, lwd=2, col=1:8) 

followed by

legend(12, 0.25, legend=filenames, lty=1, lwd=2, col=1:8)

for the RNA deg:

plotAffyRNAdeg(AffyRNAdeg(NHEK), col=1:8))

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Anna Gustafsson <annag at biotech.kth.se> 08/13/03 09:34AM >>>
Dear all,

I would be grateful if someone could help me with a small thing I am stumbling over and can not solve:

When trying to plot AffyBatch (totally 8 experiments in this case) using hist() and plotAffyRNAdeg() I can only plot multiple slides (e.g using [1:2]) but I am not able to plot just one chip. (I want to be able to tell different curves apart). 
I have tried [1] and [1:1] but get the same error message:

> library(affy)
> NHEK<- ReadAffy(widget=TRUE)
> hist(NHEK[1])
Error in apply(mat, 2, density) : dim(X) must have a positive length

I am working on windows with Rw1071 and updated all my packages from CRAN and Bioconductor yesterday from within the program.

All the best! :o)
// Anna


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Anna Gustafsson

Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

Phone (office): +46 8 553 783 41
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