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Help with complicated DESeq2 design formula
Hello. I'm familiar with DESeq2 but the most complex design equations I've used are having blocked pairs. I need to perform a more complicated design but I'm having trouble formulating the equation. I have a design table that I've read in that contains all the relevant information. Here are the specifications:
condition = sample/control (what I'm testing over)
week = a timepoint comparison of when the sample was generated
grade = a comparison of what grade of disease the sample has (so 4 > 3 > 2 > 1 > 0 ie control)
There are also 3 possible organ sites but some samples are a combination, so I've split it into 3 binary variables: is_SiteA, is_SiteB, and is_SiteC, all of which are 0 or 1
This is what the table looks like:
Right now my equation is this:
ddsHTSeq <- DESeqDataSetFromMatrix(counts_table, sample_table, design = ~ week : grade : is_GI + is_Liver + is_Skin + condition)
Is this correct at all? I really appreciate any help. FYI I do have more than 3 samples, before anyone asks!
condition = sample/control (what I'm testing over)
week = a timepoint comparison of when the sample was generated
grade = a comparison of what grade of disease the sample has (so 4 > 3 > 2 > 1 > 0 ie control)
There are also 3 possible organ sites but some samples are a combination, so I've split it into 3 binary variables: is_SiteA, is_SiteB, and is_SiteC, all of which are 0 or 1
This is what the table looks like:
Code:
sample condition week grade is_SiteA is_SiteB is_SiteC SAMPA sample 14 3 0 1 0 SAMPB control 7 0 0 0 1 SAMPC control 14 0 1 0 1
ddsHTSeq <- DESeqDataSetFromMatrix(counts_table, sample_table, design = ~ week : grade : is_GI + is_Liver + is_Skin + condition)
Is this correct at all? I really appreciate any help. FYI I do have more than 3 samples, before anyone asks!