Hi ,

I am trying to analyze a dataset with a design of one variable "sample":

gene.name;sample AB3561;dpi14bemisia AB3562;dpi14bemisia AB3563;dpi14bemisia AB3579;dpi14tocv AB3580;dpi14tocv AB3581;dpi14tocv

I have run de analysis and used contrasts in the results() to extract a results table:

>resultsNames(dds)
>contrast<- c("sample", "dpi14tocv", "dpi14bemisia")
>results<-results(dds,contrast = contrast)

The name provided in the second element ("dpi14bemisia") is the level that is used as baseline, right?

The I added thresholds:

### Set thresholds
>padj.cutoff_0.05 <- 0.05
>lfc.cutoff_0.5 <- 0.5

Subset the results table to only include those that are significant using the filter() function:

>results.table <- results%>%
  data.frame() 
#up genes padj<0.05 + fc>0.5
>up_padj_ <- results.table %>%
  filter(padj < padj.cutoff_0.05 & abs(log2FoldChange) > lfc.cutoff_0.5)
>up_padj_

But I have exactly same results if I change the order and use "dpi14tocv" as baseline

Can someone help me to understand why??

Thanks

You can use triple backticks (`) to make code blocks, I've edited your post.

If you change the order of the two levels in the contrast, the only thing that will change is the LFC and t-statistic. Check over your code very carefully if you think otherwise. Just do:

results(dds, contrast=c("condition","foo","bar"))
results(dds, contrast=c("condition","bar","foo"))

And you will see this is the case.