DESeqg design formula options

Question

[LHA_trash]

Hey guys,

I am a beginner in bioinformatics so sorry if this question may be too basic.

I am currently analyzing an RNAseq set from the GEO database. I already prepared the count matrix and the sampleinfo/metadata. I am however, struggling to create the right design formula for the DESeq object. This is the current metadata: sheet

I think I have 2 options here:

design1 <- as.formula(~celltype2*stimulation)
design2 <- as.formula(~cell_group)

The problem is, that I want to compare DC2_ctrl with DC3_ctrl and DC2_tlr with DC3_tlr. Only the second design would give me the options as result

resultsNames(ddsObj2)
[1] "Intercept"                       "cell_group_DC2_TLR_vs_DC2_ctrl"  "cell_group_DC3_ctrl_vs_DC2_ctrl" "cell_group_DC3_TLR_vs_DC2_ctrl" 

I just want to make sure, that this is the correct way to do it, because I feel like the stimulation should be a variable itself and not be grouped into the cell population. However this is the only way i get to compare my desired groups. Any advice, if I did a major mistake ?

Cheers

Answer 1

[swbarnes2]

If you want to compare one subgroup to another, design2 is the more straightforward way to do that.

[LHA_trash]

All right, i just needed reassurance that this design for DESeq is not totally wrong. Thanks!