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4 votes

How to analyse Orthofinder results

I think they simply calculate the percentage of proteins in each species that belongs to an orthogroup conserved in the five species. There should be a tab separated text file called Orthogroups....
CorteZero's user avatar
  • 109
3 votes

How to fix "No gene can be mapped, Expected input gene ID, return NULL..." error in clusterProfiler?

This issue may arise with earlier versions of clusterProfiler. A solution is to re-install clusterProfiler : ...
Basti's user avatar
  • 276
2 votes
Accepted

clusterProfiler, groupGO: meaning of GeneRatio

As you seem to be learning, the clusterProfiler package is a bit "special". It doesn't filter the results you're seeing for relevance, it returns everything. The ...
Devon Ryan's user avatar
  • 19.7k
1 vote
Accepted

groupGO parameters explanation (ont and level)

As mentioned in the comments MF is molecular function, BP is ...
Devon Ryan's user avatar
  • 19.7k
1 vote

How to fix "No gene can be mapped, Expected input gene ID, return NULL..." error in clusterProfiler?

enrichKEGG() expects entrez gene IDs so you will need to convert your gene identifiers to entrez identifiers first. EDIT: Please see the answer by @Basti.
haci's user avatar
  • 4,192
1 vote

Pathway Enrichment Analysis for one specific pathway?

Two questions Significance Lack of consistency between enzymes (log2) within the arginine and proline metabolism pathway. . 1. We've dealt with significance in a past post on Limma (it was not voom ...
M__'s user avatar
  • 12.8k
1 vote
Accepted

Interpretation of clusterProfiler results

The scenario you described would be reported by the code because: ... [abs(geneList) > 2] The abs will change any negative ...
M__'s user avatar
  • 12.8k

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