Off topic:Setting Contrast for DESeq2 results
Entering edit mode
20 months ago

I need to compare both Ly49+ versus Ly49− and MOG versus MOG plus SP. Column data in at the bottom. The function I used for DESeq2 is,

dds = DESeqDataSetFromMatrix(countData=countData,


design= ~ cell_treatment)

I am not sure if the design is right. For the results, how should I write the contrasts? I am very confused and would really appreciate any help!

DataFrame with 11 rows and 2 columns

cell treatment

<character> <character>

MOGSP_2 SPtetramer+CD8+TCell MOGSP

MOGSP_3 SPtetramer+CD8+TCell MOGSP

MOG_3 SPtetramer+CD8+TCell MOG

MOG_4 SPtetramer+CD8+TCell MOG

MOG_5 SPtetramer+CD8+TCell MOG

Ly49N_1 Ly49-CD8+TCell MOGSP

Ly49P_1 Ly49+CD8+TCell MOGSP

Ly49N_2 Ly49-CD8+TCell MOGSP

Ly49P_2 Ly49+CD8+TCell MOGSP

Ly49N_3 Ly49-CD8+TCell MOGSP

Ly49P_3 Ly49+CD8+TCell MOGSP

Thank you!!

RNA-Seq DESeq2 contrast design • 456 views
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