Entering edit mode
3.6 years ago
mahejabeen.nidhi
▴
20
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,
colData=colData,
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!!
