[BioC] Reading 'rgu34a' probeset - D37951UTR#1_at

[James W. MacDonald]

Hi Sharon,

Sharon wrote:
> Hi,
> 
> I am analysing 'rgu34a' affy chips.
> I was able to extract expression values using 'rma' and
> store the expression values in
> the 'txt' file. When, I tired to read the 'txt' file using read.table(),
> I get NA values (for all chips. but in the txt file, i do see the expression
> values) for probesets such as D37951UTR#1_at. I tried to use
> check.names=FALSE and as.is=TRUE options but not able to solve the issue.
> 
> Any suggestions?

My suggestion would be to not write the expression values to a text 
file. One of the goals of the Bioconductor project is to create and use 
data structures (such as the exprSet that originally contained your 
data) that can be used by all of the packages, and that are designed to 
contain all the information needed to track and describe the data.

By writing the data to a text file and then reading it back in, you are 
adding two completely unneccessary steps to your analysis. In addition, 
you are replacing something specific and more useful (an exprSet) with 
something general and arguably much less useful (a data.frame).

Best,

Jim


> 
> Thanks in advance.
> 
> regards,
> sharon
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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