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??