[BioC] how do I add pheno data after making AffyBatch object

[Hao Liu]

Thanks, I think I am getting there, one more question.

I got the default phenodata using

> defaultpheno <- pData(myAffyBatch);

I know I can read a data frame and assign it as pData for my AffyBatch. I 
noticed that in my defaultpheno, the first column are as

A.CEL
B.CEL
etc.........

in my read in file, however, first line is like:

A
B

etc...

the questions, do I have to make the first column the same as the default
one?  I suspect I probably have to do so since otherwise, I am afraid the
linkage will be severred.

Thank you all for your kind reply

Best
Hao

On Tue, 3 Feb 2004, Rafael A. Irizarry wrote:

> yes you can. 
> 
> first creat a phenodata object using read.phenoData (read the help file
> for more info), for example,
> 
> pd <- read.phenoData(filename="pheno.txt")
> 
> and then simply type
> 
> phenoData(abatch) <- pd
> 
> -r
> 
> here is an example of a pheno.txt file:
> 
>             label otherstuff RNA
> Empty           0          0   0
> NoRNA           1          1   0
> NotLabeled      0          1   1
> BA_polyGRNA     1          1   1
> 
> 
> On Tue, 3 Feb 2004, Hao Liu wrote:
> 
> > Dear All:
> > 
> > I used AffyBatch(), and made an AffyBatch object named A by getting all
> > the CEL files in the directory (which has about 150 cel files). However, I
> > wonder if I can add pheno object to this object after its creation.
> > 
> > And, if possible, where can I get some good tutorials on using Affy? Most
> > materials I found are hard to understand, I need some step by step or
> > examples. I am new in R and Bioconductor, please help.
> > 
> > Thanks
> > 
> > Hao Liu, Ph. D
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> 

Best regards

Hao Liu, Ph. D