Closed Rseq closed 6 years ago
How many replicates do you have per sample? Also does your dataset have more than 2 samples?
Hi, Thanks for getting back to me. My dataset has 2 samples and one replicate per sample only. Please let me know if you need more info
I would advice against trying to do differential analysis using just one replicate.
Hi, I'm aware that is not the ideal. However, is the issue due to the use of one replicate?
Yes - the plot is based on the average of the replicates. You will have to remove the rowMeans() function and just plot the norm_counts for each replicate
Yes.. it makes sense and it was so obvious. Thank you very much!
Hi,
Thank you for this package. It is working quite fine. But, I wonder if you can help me out with the differentialAnalysis. All my samples were able to pass the QC filter and the analysis ran smoothly until that part. When I call the function differentialAnalysis with the option (region="nearbait"), I have no output and the following message:
When I call the function differentialAnalysis without the option (region="nearbait"), I have no output other than a .bed file showing the regions of interaction - but no quantitative data.
I have changed the source code replacing data.frame for array, as.array, and as.matrix without success. It seems that the issue is in this region of the source code:
Do you know what is happening?
Best regards