I have the samples of two cell types (Embryo and Ovule) with two genotypes (WT and MT), which indicate as condition and genotype below. Could you please suggest how to extract information from these four combinations?
I would like to compare:
- EmbryoWT vs EmbryoMT
- OvuleWT vs OvuleMT.
- EmbryoWT vs OvuleWT
- EmbryoMT vs OvuleMT
I used the code below with model
design = ~ genotype + condition + genotype:condition to compare my samples and try to look for solutions. However, It seems to be the analysis will include the same condition or genotype together which is not our interest.
`dds <- DESeqDataSetFromMatrix(countData = clean_data, colData = meta, design = ~ genotype + condition + genotype:condition)
I highly appreciate your help.
Thanks in advance,