R help - Nov 2006 - colnames and get means for the columns with the "same" names

hi,
I have a conversion table for colnames like this:
          Probe_ID HUMAN_LLID
1  AF106325_PROBE1       7052
2 NM_019386_PROBE1       7052
3 NM_012907_PROBE1        339
4  AW917796_PROBE1      84196
5    L27651_PROBE1      10864

The Probe_ID contains a list of colnames for another data.frame, say x1.
I need to convert such colnames to another ID's system, HUMAN_LLID by
using the table. The colnames of x1 with the same names (in
HUMAN_LLID) need to be averaged. Is there a good way to do it?

I also put this question in bioconductor since I believe it might be
solved by some package.

thanks.

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

Hi, Weiwei.

You probably want to look at a combination of merge() to combine your data with
your conversion table followed by aggregate().  Read up on the help for those
two functions and that should do it, if I understand what you want to do. 
However, keep in mind that "averaging" the probesets representing the
same gene may not represent the best solution.  Also, if you search the archive
a bit, I know this question has come up before.

Sean



-----Original Message-----
From: Weiwei Shi [mailto:helprhelp at gmail.com]
Sent: Mon 11/6/2006 4:53 PM
To: r-help
Cc: bioconductor
Subject: [BioC] colnames and get means for the columns with the "same"
names
 
hi,
I have a conversion table for colnames like this:
          Probe_ID HUMAN_LLID
1  AF106325_PROBE1       7052
2 NM_019386_PROBE1       7052
3 NM_012907_PROBE1        339
4  AW917796_PROBE1      84196
5    L27651_PROBE1      10864

The Probe_ID contains a list of colnames for another data.frame, say x1.
I need to convert such colnames to another ID's system, HUMAN_LLID by
using the table. The colnames of x1 with the same names (in
HUMAN_LLID) need to be averaged. Is there a good way to do it?

I also put this question in bioconductor since I believe it might be
solved by some package.

thanks.

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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