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Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (object enrichment), nor did you show the output from `sessionInfo()`. To …
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Comment: Explannation for ROAST results by Jay • 0
Yes! Tnx for your reply. I didn't notice the group design problem, so stupid. Thank you!
Answer: Explannation for ROAST results by ATpoint ★ 4.7k
The `contrast = 2` in an intercept-less design test whether the expression in the 2nd group is not 0. You can easily solve this by using `~…
Comment: Explannation for ROAST results by Jay • 0
BTW, AP1 is a character, composed of gene entrez ID, so is HIF1, UPR, etc al. And the rownames of `expr.i` is also gene entrez ID.
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Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
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