[BioC] Annotate Package: How do I get the gene names and how do I write my matrix

[James MacDonald]

If you are planning on using R for any more analysis, you would do well
to read some of the documentation that comes with R and the BioC
packages rather than hoping that a good samaritan will help you do
things.

1.) Look at the documentation for the annaffy package
2.) Read 'An Introduction to R'
3.) Read 'An Introduction to R'

All of this information is easily accessible by typing help.start() at
an R prompt.

Best,

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

>>> S Peri <biocperi at yahoo.com> 08/18/04 01:54PM >>>
Dear group, 

I did SAM, T-test analyses and obtained p-values. Now,
these files look like these:

T-test Values:

> Gli_X0_X1_pvals[1:5]
  100_g_at    1000_at    1001_at  1002_f_at  1003_s_at

0.80033009 0.31943016 0.33078591 0.05216239 0.08957325



Fold change(Avg. Diff):
> MyBrain_X0_X1_Exp_FCs[1:5]
 100_g_at   1000_at   1001_at 1002_f_at 1003_s_at 
1.0176023 0.9274588 0.8752550 1.1056984 1.1096023 


My question: 

Using annotation package how can I convert the probe
ID's to Gene names. how do i incorporate gene name in
place of 100_g_at?


2.  How can I choose/filter P-values from T-test that
are less than 0.01 to 0 ?


3. How can write the values into a table with 3
colnames:
Gene, P-value, Fold change

I am doing this for first time. Please help me. 

Thank you.

Regards, 
PS

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