Combine different microarray datasets of the same chip with limma

Question

[teresa.noviello89]

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 withinArray and then also the betweenArray one. Is it correct?

Answer 1

[Manvendra Singh]

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

[teresa.noviello89]

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