I have a total of 8 samples, 4 controls and 4 Foxcut gene over expressed samples.
The column data for all the 8 samples look like below with replicate and cell-line information:
Samples TYPE Replicate Cell-lines Cell1_HA1 Control 1 1 Cell1_HA2 Control 2 1 Cell1_foxcut11 FOXCUT_OverExpression 1 1 Cell1_foxcut12 FOXCUT_OverExpression 2 1 Cell2_HA1 Control 3 2 Cell2_HA2 Control 4 2 Cell2_foxcut11 FOXCUT_OverExpression 3 2 Cell2_foxcut12 FOXCUT_OverExpression 4 2
I have counts data for all the 8 samples after
star alignment. I'm using
edgeR package for differential analysis. This is the first time I'm doing differential analysis with cell-line data with replicate information. I'm not aware about how to create
design matrix and
contrast.matrix for differential analysis between different samples.
I wanted to compare the below samples and do differential analysis:
Cell1_foxcut samples vs Cell1_HA samples Cell2_foxcut samples vs Cell2_HA samples
Can anyone please help me how to group the samples and how to create design matrix and how to mention
coef for differential analysis between different samples.