Thank you.
Yhe I would like to use RMA but for now I'm trying to repeat someone former results.
The problem is that I am getting twice as many genes.
And the expression values are extremely different.
Why is the scaling so random and different from the one done by affymetrix MAS5?
Cheers, 
Liat.

Date: Thu, 12 Jul 2012 11:49:13 -0400
Subject: Re: [BioC] Affy mas5 scaling
From: chenyao.bioinfor@gmail.com
To: liats80@hotmail.com
CC: bioconductor@r-project.org

Hi Liat,
Personally, I will use RMA instead of MAS5 to normalization affy data.
It's quite normal when you use different parameter in normalization, you get different number of genes. But it's not a big problem. I would expect highly overlap of these two sets of genes.

Jack

2012/7/12 Liat S <liats80@hotmail.com>



Hi all,

I have some raw data as well as Affymetrix MAS5 normalized data for oligonucleotide arrays.

For the raw data I use the mas5 function of the affy package.

>From then on I run the same code on both (removing AFFY controls, applying log, selecting genes over a certain fold change etc.).

I end up with different numbers of genes...

I have done A LOT of debugging (including doing the same actions manually in excel :o/ ) and am quite convinced now that the difference has to do with the normalization itself.

The values of normalized data are very different, with the R normalized data having much higher values.

I noticed that the mas5 function in the Affy package uses 500 as a scaling value.

Can that be the source of the difference I see?

Is there anyway to better approximate the MAS5 scaling?

Thanks!

Liat.

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