[BioC] Order in which ReadAffy() and read.affybatch()

[James W. MacDonald]

Hrishikesh Deshmukh wrote:
> Hello All,
> 
> I have questions about the order in which ReadAffy()
> and read.affybatch() reads in affy CEL files. I need
> this piece of information because i want to label the
> arrays when i look at hist() and boxplot(). I want to
> make sure that right labels (filenames) are displayed
> for its corresponding lines/boxplots. 

Samples are read in alphanumeric order. In your case this would be 
1.CEL, 10.CEL, 11.CEL, 12.CEL,... If you want them to be read in the 
same order as your file.names list, you need to prepend a zero on all 
the celfile names that have a single digit (e.g., 01.CEL, 02.CEL, etc).
> 
> Is there a book specifically on BioC, this would be a
> big help?
> 
> In general on what basis does one accept/reject arrays
> from a pool of replicates! The hist() and boxplot()
> shows clearly that all the arrays (replicates) do not
> show the same "behaviour".
> 
> Here are the code fragments:
> library(affy)
> library(hgu95av2cdf)
> library(hgu95av2probe)
> library(matchprobes)
> data(hgu95av2probe)
> summary(hgu95av2probe)
> file.names<-c("1.CEL",  "2.CEL",  "3.CEL",  "4.CEL", 
> "5.CEL","6.CEL","7.CEL",  "8.CEL",  "9.CEL", 
> "10.CEL", 
> "11.CEL","12.CEL","13.CEL",14.CEL","15.CEL","16.CEL","17.CEL")
> M<-read.affybatch(filenames=file.names,
> description=NULL,notes="",compress=F,   
> m.mask=F,rm.outliers=F,rm.extra=F,verbose=T)
> hist(M)
> legend(12,1.2,sampleNames(M),col=1:17,lty=1:17) 

Note that col=1:17 is the same as col=c(1:8, 1:8, 1). If you want more 
colors, you will have to resort to actual color names (there are 
hundreds of those, see colors()).

Also note that if you want the density plots and legend to match, you 
have to supply the same variables to both.

hist(M, lty=c(rep(1,8), rep(2,8), 3), col=1:17)
legend(12, 1.2, sampleNames(M), col=1:17, lty=c(rep(1,8), rep(2,8), 3))

> 
> When i run the legend line i see hist() displays
> different "lines" and legend does not match correctly!
> 
> Thanks in advance.
> Hrishi
> 
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-- 
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