I analyzed my data using DESeq - 4 samples - in duplicates - for a total of 8. While I was able to pull out several DE genes, the plots look odd - attached. Please let me know your thoughts.
Also, initially, I did not have replicates and ran the analysis on just 4 samples. Oddly, my analysis with the replicates - for one pair - pulled out a lot more DE genes but primarily downregulated. I would not expect there to be such a bias towards downregulated genes only with the technical replicates - does this strike anyone as abnormal?
Attached is a venn diagram depicting how my initial analysis without replicates compared with my second analysis with replicates - oddly, there is very little overlap between the genes upregulated from the initial analysis (no rep) compared to with rep. Please give me your input as this is quite disturbing to me!
Finally, where can I find options to play around with the DESeq plot - ie. add a title, change colors etc.
I am a novice in this field so your input would be much appreciated.
Thanks!
Also, initially, I did not have replicates and ran the analysis on just 4 samples. Oddly, my analysis with the replicates - for one pair - pulled out a lot more DE genes but primarily downregulated. I would not expect there to be such a bias towards downregulated genes only with the technical replicates - does this strike anyone as abnormal?
Attached is a venn diagram depicting how my initial analysis without replicates compared with my second analysis with replicates - oddly, there is very little overlap between the genes upregulated from the initial analysis (no rep) compared to with rep. Please give me your input as this is quite disturbing to me!
Finally, where can I find options to play around with the DESeq plot - ie. add a title, change colors etc.
I am a novice in this field so your input would be much appreciated.
Thanks!
Comment