I also read in vignette and many post about multiple factor design but I still don't get it.What I want is to compare between the same cell type and also in the same day but different in heat condition. For example

Day0cellABCheatC VS Day0cellABCheatH

So I design a condition as follow which I'm not sure it correct or not.

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
                                       directory = dir,
                                       design= ~ ~ cell+Day+heat+cell:heat)

here is my data look like

as.data.frame(colData(dds))


                          Day cell heat sizeFactor
D0_ABC_C1.sort_new_count   D0  ABC    C  0.7940138
D0_ABC_C2.sort_new_count   D0  ABC    C  1.2122551
D0_RST_C1.sort_new_count   D0  RST    C  1.1625389
D0_RST_C2.sort_new_count   D0  RST    C  1.0165686
D13_ABC_C1.sort_new_count D13  ABC    C  0.8062614
D13_ABC_C2.sort_new_count D13  ABC    C  0.7919916
D13_ABC_H1.sort_new_count D13  ABC    H  0.5067959
D13_ABC_H2.sort_new_count D13  ABC    H  3.0570842
D13_RST_C1.sort_new_count D13  RST    C  0.1802654
D13_RST_C2.sort_new_count D13  RST    C  0.9946196
D13_RST_H1.sort_new_count D13  RST    H  4.9916143
D13_RST_H2.sort_new_count D13  RST    H  1.2102286
D6_ABC_C1.sort_new_count   D6  ABC    C  2.4271542
D6_ABC_C2.sort_new_count   D6  ABC    C  0.8863761
D6_ABC_H1.sort_new_count   D6  ABC    H  1.0265614
D6_ABC_H2.sort_new_count   D6  ABC    H  0.6471705
D6_RST_C1.sort_new_count   D6  RST    C  2.8035811
D6_RST_C2.sort_new_count   D6  RST    C  0.9791049
D6_RST_H1.sort_new_count   D6  RST    H  0.7122750
D6_RST_H2.sort_new_count   D6  RST    H  0.5222761

and the resultsNames(dds) is

"Intercept"       "cell_RST_vs_ABC" "Day_D13_vs_D0"   "Day_D6_vs_D0"    "heat_H_vs_C"     "cellRST.heatH" 

My question is if I want to select the result like Day0cellABCheatC VS Day0cellABCheatH and Day6.cellABC.heatC VS Day6.cellABC.heatH. How do I get the result that I want

I try the following command but it give me an error

res<-results(dds, contrast = list(c("DayD13.cellABC.heatC","DayD13.cellABC.heatH")), alpha=0.05)

Error in checkContrast(contrast, resNames) :
  all elements of the contrast as a list of length 2 should be elements of 'resultsNames(object)

See this part of the vignette. If you want to test pairs of combinations of all factors, it's best to combine the variables into a single factor, group. You can produce the same design using interactions, but many users find it difficult to build the contrasts, whereas it's trivial when you combine them into 'group'

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions