How to use limma packet for Chip data difference Analysis

This article mainly introduces how to use the limma package for chip data difference analysis related knowledge, the content is detailed and easy to understand, the operation is simple and fast, has a certain reference value, I believe that everyone after reading this article on how to use the limma package for chip data difference analysis will have a harvest, let's take a look.

Using limma packet to analyze chip data difference, it is necessary to construct a packet matrix according to the packet information, which is completed based on the model.matrix function. The structure of the packet matrix obtained is similar to the result shown below:

> design A BGSM1626001 1 0GSM1626002 1 0GSM1626003 1 0GSM1626010 0 1GSM1626011 0 1GSM1626012 0 1attr (, "assign") [1] 1 1attr (, "contrasts") attr (, "contrasts") $`promotion` [1] "contr.treatment"

The 01 indicates whether there are three GSM1626001 GSM1626002 GSM1626003 samples in group A, but the understanding of group B is the same. The whole matrix describes the two groups of samples to be compared, and then the difference comparison matrix is constructed by makeContrasts to continue the follow-up analysis.

ContrastsLevels B-An A-1 B 1

Indicates the beginning of differential expression analysis of group B relative to group A.

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