How To Scale The Expression Data Of Affy To A Same Average Intensity

Question

[J.F.Jiang]

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

[Neilfws]

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

[J.F.Jiang]

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

[Neilfws]

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.

[J.F.Jiang]

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

plz take a look at this,

Answer 1

[Damian Kao]

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

[J.F.Jiang]

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