User: markm014

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markm0140
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Posts by markm014

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Comment: C: ClusterProfiler dotplot method does not include all input groups.
... Thank you for taking the time to answer. The thing is, when I run the enrichGo function on each of the 8 input groups separately with the same parameters, they all 8 have significant GO terms. Sorry, I should have included this above! ...
written 7 weeks ago by markm0140
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ClusterProfiler dotplot method does not include all input groups.
... I am using the clusterProfiler methods enrichGO and dotplot to do some downstream differential expression analysis. I invoke enrichGO with the following call: > formula_res = compareCluster(`EntrezGene ID~Direction+Treatment, data=filtered_data, fun="enrichGO", OrgDb="org.Hs.eg.db", ont="BP", qv ...
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Comment: C: Using featureCounts Output for DE analysis in edgeR
... Thank you a bunch, this worked like a charm. For anyone trying to replicate this solution, note that you should not use quotes when dropping columns using '-c'. ...
written 19 months ago by markm0140
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Using featureCounts Output for DE analysis in edgeR
... I am getting the following error in R studio when I attempt to import featureCounts count matrices into edgeR for analysis. **My question is, do I have to manually modify the output of featureCounts for use in edgeR?** Everywhere I look within documentation, it makes it seem as if I can directly loa ...
featurecounts rna-seq edger written 19 months ago by markm0140 • updated 19 months ago by Friederike6.2k

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Popular Question 18 months ago, created a question with more than 1,000 views. For Using featureCounts Output for DE analysis in edgeR

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