[BioC] Missing name header in rma

[James MacDonald]

What you are seeing is due to the fact that the probeset IDs are saved
in the expression matrix as row names. When you export to a text file,
there is no column name for the row names, so you just get an empty
cell. You can automatically shift the column names over by adding
col.names=NA to your write.exprs arguments.

However, if you are planning to analyze your data using R or
Bioconductor, you can simply avoid the whole export/import problem
altogether. If you are using Bioconductor, the data is already in an
exprSet, which is what almost all of the packages will expect. If you
are planning to do your analysis in R without using Bioconductor, you
can export to a matrix by doing something like 

my.data <- exprSet at exprs (you will have to substitute the actual name
of your exprSet).

Regards,

Jim



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

>>> "Haddad, Ramsi" <Ramsi.Haddad at vai.org> 07/11/03 10:22AM >>>
Howdy,
 
    I'm just starting out, so forgive me if this sounds silly.  I was
following the example in the "textual description of affy" to normalize
my data with rma and then wrote out the file.  When I opened the results
in excel, the column header was missing on the final column.  The column
header for probset name was actually the name of the first array.  When
I normalized using RMAexpress, I could see that the problem was that the
probset name was missing and all the names of the arrays were shifted to
the left.  Should I simply insert the probeset column header in excel
and import  the file back into bioconductor to continue my analysis?  I
am using the most recent version of bioconductor in linux which I
downloaded a few weeks ago.
 
thanks,
 
Ramsi
 

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