Question: Normalization across different tissues for Affymetrix Array
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gravatar for shirley zhang
12.3 years ago by
shirley zhang1.0k
shirley zhang1.0k wrote:
Dear Bioconductor: We run Affy's all exon array on 3 tissues (lung, nose, and mouth). For each tissue, 10 samples are in control and 10 in treatment group. Totally 60 samples. General speaking, the sigal from lung is similar to that of nose, and the signal from mouth is much lower than lung and nose. I've tried the following normalization: Method 1. Quantile Normalize all 3 tissues together Method 2. Quantile Normalize each tissue separately Method 3. Quantile Normalize each tissue separately, and then do Global Median aross all My question is: in order to do 2-way ANOVA including the interaction term between tissue and treatment, which normalization method is applicable? Thanks, Shirley
normalization lung • 438 views
ADD COMMENTlink written 12.3 years ago by shirley zhang1.0k

Hi Shirley,

I know that I'm replying to the post written 8,7 years ago, but I have the same problem as the one described here. I'm wondering if you finally got your answer and are willing to share it?

Regards,

Kasia

 

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by katarzyna.kolanek0
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