Question: How To Scale The Expression Data Of Affy To A Same Average Intensity
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gravatar for J.F.Jiang
6.3 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

Hi all,

I am processing the expression data from GEO to make a further step of analysis “All arrays were scaled to the same average intensity (200).” I am curious how to make this step

Thanks

expression affymetrix • 1.6k views
ADD COMMENTlink modified 6.3 years ago by Damian Kao15k • written 6.3 years ago by J.F.Jiang750

Would help to link to the GEO accession so we can see this statement in context.

ADD REPLYlink written 6.3 years ago by Neilfws48k

actually, i want to compare two different expression datasets, which I think should pre-process them to same level. And finally I combine them together to do the quantile normalization to what I want.

Thnaks anyway

ADD REPLYlink written 6.3 years ago by J.F.Jiang750

It would still be helpful to link to the source of the statement "“All arrays were scaled to the same average intensity (200)”, so we can see exactly what they are talking about.

ADD REPLYlink written 6.3 years ago by Neilfws48k

http://geschwindlab.neurology.ucla.edu/index.php/protocols/32-rtutorial2

plz take a look at this,

ADD REPLYlink written 6.3 years ago by J.F.Jiang750
2
gravatar for Damian Kao
6.3 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

So I assume you are trying to center your data to 200.

It's similar to a standardization where you subtract the mean of the samples across your samples to get a constant mean of 0.

To get a constant mean of 200, you can add (200 - mean) across your samples. For example if one of your rows look like this:

geneX   50   10   20   40

The mean for this gene is 30. To make the mean 200, you just add a constant of 170 (200 - mean) to each number:

geneX   220  180  190  210
ADD COMMENTlink written 6.3 years ago by Damian Kao15k

Thanks, I think I am going to scale the array not the genes. OR scale the sample to the average density to 200 but not the genes

ADD REPLYlink written 6.3 years ago by J.F.Jiang750
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