Entering edit mode
22 days ago
xiaoyongli407
•
0
Hi, I have ran an sdgeR analysis for a set of RNA-Seq samples from an RNAi knockdown experiments - there are 3control and 3 treatment samples. Strangely, in the run results all the genes have huge negative logFC values. Do you know what might have gone wrong with the analysis?
Please show code and plots, words alone cannot help debugging.
More details would be helpful, but it sounds like you are looking at the wrong comparison/contrast. For example, this is what I would see if I compare control to itself.
For example, my design compares condition to control. The control is represented by coefficient 1 and condition is coefficient 2. With the way I setup the design when I run the test and specify
coef = 2
it will compare condition to control. If I compare control to itself bycoef = 1
it is not proper and results in very low fold-changes