Matthew Hannah Hannah at mpimp-golm.mpg.de
Thu Mar 24 10:25:16 CET 2005

```Hrishi,

The bioC documentation, "introduction to R", short courses, BioC archive
search and normal google reward the persistent.
Here's a couple of pointers that may also help.

#r ignores anything on the same line following a #
help.start() # starts html help
#?any command - opens the documentation eg:
?par #all you need to know for controlling and labelling graphs

library(affy)
#Getting your filenames and removing .CEL
sampleNames(data)
un <- ".CEL"
sampleNames(data) <- gsub(un, "", sampleNames(data))
#Look at plots of log2 raw intensity
hist(data, lwd=2, lty=1, col=rainbow(25), main = "Chip raw intensity")
legend(13, 0.4, legend=sampleNames(data), lty=1, lwd=2, col=rainbow(25))
boxplot(data, col=rainbow(25),las=2)

#now look at RMA normalized data
eset <- rma(data)
boxplot(exprs(eset))
boxplot(as.data.frame(exprs(eset)),col=rainbow(25),las=2)

#compare expression between samples
par(mfrow = c(2, 2))
x <- exprs(eset)
plot(x[,1], x[,2], pch=".", main="Sample 1 vs 2", xlab="RMA exprs sample
1", ylab="RMA exprs sample 2")
abline(0,1,col="Red")
plot(x[,1], x[,3], pch=".", main="Sample 1 vs 2", xlab="RMA exprs sample
1", ylab="RMA exprs sample 3")
abline(0,1,col="Red")
plot(x[,2], x[,3], pch=".", main="Sample 1 vs 2", xlab="RMA exprs sample
2", ylab="RMA exprs sample 3")
abline(0,1,col="Red")

history(50)

##############
Hi All,

I am not that familiar with BioC terms, i know
CEL file and two "different" kinds of objects are
created and typically some "kinds" of analyses for
example boxplot() may work with readaffy() and not
with read.affybatch() and hist() might work well with
read.affybatch()!! But these are the kinds of
questions for which docs are non-existant! Vignettes
help but they only whet your appetite but do not
satisfy your hunger!! Sorry went in different
direction.

I do work with multiple OS and thanks for the piece of
very important information. One simple way to make
sure no matter what order the files are read, doing
simple hist() and/or boxplot() and then making sure
that right labels(filenames) are given for the
lines/plots.....now to do this simple thing one has to
go through lot of documentation! Ahhh!!!

Is there a book on BioC specifically which will help
people be conversant with terms and use it
efficiently!!!

But hats off to the mailing list members for answering
my simple/naive questions.

Regards,
Hrishi

```