How to do median polish among three tables

shuang · 04-13-2012, 12:26 PM

I have 3 tables (derived from microarray datasets by gcrma normalization).

I want to perform "median polish" on these 3 tables. Basically, I want to make their median the same by proportionally modify the values in each table.

Which function/command can do this?

westerman · 04-16-2012, 07:31 AM

Seems easy enough to program in Python/Perl/whatever if that is your cup of tea. I suspect 'R' has a function although I am not that familiar with 'R'. Galaxy or one of the other platforms ... hard to say.

I suspect that you would get more of a response if you would tell us what tools you are comfortable with and what format your microarray data is in. Since you used gcrma normalization then I suspect you are using R/bioconductor or perhaps matlab.

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04-13-2012, 12:26 PM	#1
shuang Senior Member Location: IL Join Date: Jul 2011 Posts: 100	How to do median polish among three tables I have 3 tables (derived from microarray datasets by gcrma normalization). I want to perform "median polish" on these 3 tables. Basically, I want to make their median the same by proportionally modify the values in each table. Which function/command can do this?

04-16-2012, 07:31 AM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	Seems easy enough to program in Python/Perl/whatever if that is your cup of tea. I suspect 'R' has a function although I am not that familiar with 'R'. Galaxy or one of the other platforms ... hard to say. I suspect that you would get more of a response if you would tell us what tools you are comfortable with and what format your microarray data is in. Since you used gcrma normalization then I suspect you are using R/bioconductor or perhaps matlab.