Hej, im a microbiologist working in my master and I accidently blurted out I took basic bioinformatic as a course and now wants some help with some 39k data entries (my terminology is not the greatest)

Im working on a larger dataset the count matrix looks like this

genes |A.1|A.2|A.3|A.4|B.1|B.2|B.3|B.4|C.1|C.2|C.3|C.4|D.1|D.2|D.3|D.4
AT5G   *imagine a bunch of numbers here  
AT6G
AT7G
AT8G
AT9G 


coldata <- data.frame(sample = c(rep("A", 4), rep("B", 4), rep("C", 4),rep("D", 4)),
                 timestamp = c(rep("1",1),rep("2",1),rep("3",1),rep("4",1)))

which looks like this
sample   timestamp
<chr>    <chr>
A       1           
A       2            
A       3           
A       4           
B       1
B       2           
B       3       
B       4       
C       1           
C       2
C       3           
C       4       
D       1       
D       2    
D       3   
D       4

and this is my

DESeqDataSetFromMatrix

dds_sub <- DESeqDataSetFromMatrix(countData = count_matrix, colData = coldata, design = ~ sample + timestamp)

as you can se in my resultnames(dds.sub)

resultsNames(dds_sub)
[1] "Intercept"                              "sample_dcp5_vs_Col.0"                  
[3] "sample_pat1.path1.path2.summ2_vs_Col.0" "sample_summ2_vs_Col.0"                 
[5] "timestamp_CIM_24hr_vs__NT_0min"         "timestamp_CIM_45min_vs__NT_0min"       
[7] "timestamp_CIM_6d_vs__NT_0min"  

I only get options for sample or for timestamp

what I need is sample AND timestamp specifically

sample_A.2_VS_B.2

but R keeps spitting this error after me

Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, :A 2 and B 2 should be levels of sample such that sample_A.2_vs_A and sample_B.2_vs_A are contained in 'resultsNames(object)'

I'd recommend to pair up with someone who can help you formulate the design and specify how to pull out the right terms. Unfortunately I only have time to help with software related issues here. Besides avoiding errors, you also want to make sure you understand the meaning of the contrasts you are performing.