Dear everyone,
I am going through my first RNA-seq analysis, where I am starting off using the Trapnel et al, 2012 paper.
I noticed that when I have three different conditions, then the density plot does not contain any -log10(fpkm) values, whereas when I add to extra conditions, then the plot looks completely different.
I am uncertain how to interpret these results whether I can trust them or not.
/Update: By adding these two extra samples, I go literally from 3xx DE genes to very, very few. I guess this is because the more samples you add that are different from each others, the more less likely you are to see subtle changes between the other samples.
Thanks a lot! I appreciate your help.
I am going through my first RNA-seq analysis, where I am starting off using the Trapnel et al, 2012 paper.
I noticed that when I have three different conditions, then the density plot does not contain any -log10(fpkm) values, whereas when I add to extra conditions, then the plot looks completely different.
I am uncertain how to interpret these results whether I can trust them or not.
/Update: By adding these two extra samples, I go literally from 3xx DE genes to very, very few. I guess this is because the more samples you add that are different from each others, the more less likely you are to see subtle changes between the other samples.
Thanks a lot! I appreciate your help.