Multiple conditions DESeq2

Question

[judhenaosa]

Hi,

I am working on differentially expressed genes analysis of RNA-seq data extracted from multiple but related experiments:

experiment

DESH21_E
DESH40_S
DESN21_E
DESN21_S
DESN40_E
DESN40_S
ES21_E
ES21_S
ES40_E
ES40_S

where, DES and ES are different in vitro cells; 21/40 are concentration (low/high), and H/N are additional stress (high/normal). All experiments have three replicates.

I want to use DESeq2 and compare several experiments, for example:

1. DESN21_E vs DESH21_E
2. DESN21_E vs DESN21_S
3. DESN40_S vs DESN40_E
4. DESN40_S vs DESH40_S

However, DESeq2 takes only the first level in the metadata to perform the comparisons.

An example:

dds <- DESeqDataSetFromMatrix(countData = counts,
                          colData = meta,
                          design = ~experiment)

dds <- DESeq(dds)
resultsNames(dds)

 [1] "Intercept"                       "experiment_DEH21_vs_DESH21_S"    "experiment_DEH40_vs_DESH21_S"   
 [4] "experiment_DEN21_vs_DESH21_S"    "experiment_DEN40_vs_DESH21_S"    "experiment_DESH21_E_vs_DESH21_S"
 [7] "experiment_DESH40_S_vs_DESH21_S" "experiment_DESN21_E_vs_DESH21_S" "experiment_DESN21_S_vs_DESH21_S"
[10] "experiment_DESN40_E_vs_DESH21_S" "experiment_DESN40_S_vs_DESH21_S" "experiment_E21_vs_DESH21_S"     
[13] "experiment_E40_vs_DESH21_S"      "experiment_ES21_E_vs_DESH21_S"   "experiment_ES21_S_vs_DESH21_S"  
[16] "experiment_ES40_E_vs_DESH21_S"   "experiment_ES40_S_vs_DESH21_S"   "experiment_S21_vs_DESH21_S"     
[19] "experiment_S40_vs_DESH21_S" 

How can I use the whole count matrix and perform the different comparisons without re-run DESeq changing the levels in the metadata to carry every comparison?

Thanks in advance,

Juan

[antonioggsousa]

Hi,

If you only want to get pairwise comparisons, then you can use contrasts as described in the DESeq2 manual: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#contrasts

António

Answer 1

[swbarnes2]

As the comment says, you can use contrasts to compare whatever you want, even if what you want is not in ResultsNames