[BioC] Incompatible phenoData object. Created a new one.

James MacDonald jmacdon at med.umich.edu
Sat Mar 26 01:54:03 CET 2005

Hi Salil,

This is just a simple misunderstanding. What you have to understand is
that you are instantiating an AffyBatch object that has different
'slots' that can contain different information (type class ?AffyBatch at
an R prompt for more information). There is a slot (the pData slot) that
can contain a data.frame() that lists out the phenotypic data for your
different samples. Since you didn't specify anything, read.affybatch()
made something up for you. If you type pData(data), you will see what is
in that particular slot.

Note here that 'data' is a bad variable name because you are masking an
existing R function called data(). I prefer to use e.g., dat, or Data.

Since the AffyBatch is an object with several slots, dim(data) doesn't
make any sense, so you get NULL returned. There are several accessor
functions that can be used to look at the data contained in your
AffyBatch. Again, see class ?AffyBatch for more information.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> SALIL SHARMA <ssharma at jhmi.edu> 03/25/05 5:08 PM >>>
Hello group,

Iam a  novice in microarray data analysis.

I am using R version  2 and Bioconductor version 1.5.

My experiment is to read some cel files from a directory and to derive
expression values.

> library(Biobase)
> library(affy)
> data <-
Warning message: 
Incompatible phenoData object. Created a new one.
 in: read.affybatch("3AJW02021805_lung.CEL", "3AJZ02021909_HEART.CEL",  
 > dim(data)

I do not understand this problem.  I have seen my friend using R version
1.9 has no problem with same files.  Is this a bug in R 2.0 or  am i
committing a mistake here.  
Could any one help me , please. 

Thank you.


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