Bioconductor Factominer

Showing : factominer • reset

4

votes

6

replies

1.6k

views

deseq2 factominer PCA

updated 8.2 years ago by Ryan C. Thompson ★ 7.9k • written 8.2 years ago by sebastiano.curreli • 0

1

vote

3

replies

1.4k

views

Biplot FactoMineR proteomics PCAtools ellipse

updated 20 months ago by Kevin Blighe ★ 4.0k • written 20 months ago by M Tuhin • 0

0

votes

1

reply

2.0k

views

clustering r fpc FactoMineR

5.1 years ago anahochmanova • 0

0

votes

5

replies

4.4k

views

software error factomineR bioclite

updated 9.3 years ago by Martin Morgan 25k • written 9.3 years ago by dany_wm44 • 0

4 results • Page 1 of 1

Recent ...

Replies

Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k

In the other thread I pointed out that filtering on the p-value AND the logFC is fraught because you are mixing population parameter estima…

Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k

The way you are doing it includes all three ontologies. Unless you used "ALL" as the ontology, the number of genes annotated should be less…

Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10

Thank you very much for helping a beginner. To your point, I did that, so there are two pieces of evidence which don't quite compute: If …

Answer: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k

The default for `testEnrichment` is a one-tailed test. If you want a two-tailed test you have to specify that.

Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10

Thank you Luís, I just did put it's just: KYCG_plotVolcano(results,label_by="gene_name",alpha=0.01) (if I understand what you wanted), but …

Votes

Answer: object 'hdac_targets' not found

Answer: In the sesame package, what does the estimate output mean from testEnrichment()

C: Usability of ERCC spike-ins in standard RNAseq experiments

A: Usability of ERCC spike-ins in standard RNAseq experiments

Awards • All

Scholar to James W. MacDonald 67k

Teacher to Aaron Lun ★ 28k

Popular Question to Robert Castelo ★ 3.4k