```

Hi all

I have a single cell data experimental design which looks like this:

cluster_metadata

Sample_N   Condition    Treatment  Sample_ID Sample_Name
1            healthy        untreated          S1                 H1
2            healthy        treated              S1                 H2
3            healthy        untreated          S2                 H3
4            healthy        treated              S2                 H4
5            healthy        untreated          S3                 H1
6            healthy        treated              S3                 H2
7            healthy        untreated          S4                 H3
8            healthy        treated              S4                 H4
9            disease       untreated          S5                 DB1
10          disease       treated              S5                 DB2
11          disease       untreated          S6                 DB3
12          disease       treated              S6                 DB1
13          disease       untreated          S7                 DB2
14          disease       treated              S7                 DB3

I have 4 healthy individuals (S1,S2,S3,S4) and 3 individuals with disease (S5,S6,S7) which have been treated or not treated with a drug and I would like to determined the effect of the drug treament. It is a paired experimental design since the same individual has been treated or not treated with the drug. I have run some analysis and obtained a count matrix (cluster_counts) reached to the point where I have to design a formula:

dds <- DESeqDataSetFromMatrix(cluster_counts, 
                              colData = cluster_metadata, 
                              design = ~ sample_Name + Treatment )

However, this formula does not seem correct as I see wrong comparisons in the output.

After running :

dds <- DESeq(dds)
resultsNames(dds)

it gives:

> resultsNames(dds)
[1] "Intercept"                  "Sample_Name_DB2_vs_DB1"              "Sample_Name_DB3_vs_DB1"             
[4] "Sample_Name_H1_vs_DB1"               "Sample_Name_H2_vs_DB1"               "Sample_Name_H3_vs_DB1"              
[7] "Sample_Name_H4_vs_DB1"               "condition_treated_vs_untreated"

What is the correct formula in this experimental design? Thanks