[BioC] Expression values of a gene

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Wed Feb 9 01:06:32 CET 2005

Dear group:

I have a couple of questions. 


I have 250 CEL files from various experimental
sources. My aim is to extract gene expression values
(and not the fold changes) for every gene on
chromosome 17.

I obtained the gene expression values in the following

my_expr_values <-exprs(justRMA())

Is it true that I have expression values for all the
probesets in my_expr_values?

Or did I miss any crucial step here.

Question 2:

For many genes affymetrix assigned 2 or more
For egfr gene there are 4 probe_sets. 

Now that I want expression values for 'single gene',
what do I have to do to assign an expression value to
a single gene.  Does the program averages the
experssion values for 4 probe_sets and assigns a
single expression value to EGFR gene?

3 Question:

How can I obtain genes on chromosome 17. 

my_chr_list <- as.list(hgu133aCHR)
my_gene_name <- as.list(hgu133SYMBOL)

How can I associate the gene_name to the probe_set
(with Expression values) and chromosome number. 

Can any one please help me. Thank you.  Srini

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