Question: Combine different microarray datasets of the same chip with limma
0
gravatar for teresa.noviello89
6.0 years ago by
Italy
teresa.noviello890 wrote:

Hi, I have 3 different datasets of micrarray experiments (two about TF's overexpressions and one about TF's repression ). They are from the same platform Agilent. I have to create a meta-matrix combining them and i'm trying to use the limma package. First i have read each of them separatly and then combine the RGLists for the normalization withinAraay and then also the betweenArray one. Is it correct?

R • 1.7k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by teresa.noviello890

Thank you:) I'm trying to do as you suggest

ADD REPLYlink written 6.0 years ago by teresa.noviello890
1
gravatar for Manvendra Singh
6.0 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

I would suggest you to just merge your three dataframes by genenames/Agilent ID then transform their expression value on log2 scale.

Afterwards, if you are using limma then there is function to normalize them which is normalizeQuantiles {limma}. draw a boxplot to see if data is normalized. Your meta-matrix is ready for your analysis.

 

HTH

ADD COMMENTlink written 6.0 years ago by Manvendra Singh2.1k
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