Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?

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ashwinmenon1994 • 0

@ashwinmenon1994-23231

Last seen 4.1 years ago

Hi everyone, I am trying to make a design matrix and contrast matrix to conduct Limma on the microarray data. I have 12 samples, 3 hours wild type (3x), 24 hours wild type (3x), 3 hours treatment (3x) and 24 hours treatment (3x). I want to compare the differentially expressed genes between the control and wild type in all time course and also in between time course (3 hours and 23 hours), to see how they differ. What do you think the best way to go about this is ?

limma R microarray timepoint affy • 584 views

ADD COMMENT • link updated 4.1 years ago by shepherl 3.8k • written 4.1 years ago by ashwinmenon1994 • 0

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Hello. What have you already tried?; what data do you currently have (presumably CEL files)?; where have you looked (online) about how to do this? Limma is one of the most widely- and often-used programs of all time in bioinformatics; so, there is ample material (tutorials, code examples, etc) online such that you should be able to reproduce what you want.

ADD REPLY • link 4.1 years ago Kevin Blighe ★ 3.9k

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