understanding similarity in different sra files

Question

[biology_inform]

Hi all, I have a logical question. I took a dataset from GEO (GSE121634). I analyzed samples separately. For example: 827Parental vs 827ER1 827Parental vs 827ER3 827Parental vs 827ER6 4006Parental vs 4006ER1... I analyzed all like this so I have 8 different DGE list. But I want to learn how they are different from each other (For example: 827Parental vs 827ER1 and 827Parental vs 827ER3 827Parental vs 827ER6 if they are different from each other or not)

I tried to plot PCA plot but I couldnt figure out the logic behind.

[swbarnes2]

You compared one sample to one sample? That's not particularly meaningful. The reason they did three replicates for each condition is you are supposed to groups of samples to each other.