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Results tagged with limma
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user 3225
0
votes
1
answer
115
views
Single sample in group: normal pipeline or Kal's Z test
When I say normal pipeline I mean limma-voom, edgeR and DESeq2 pipeline for standard analysis. … So my main questions are:
(1) when using limma/edgeR/DESeq2, should the model design include all the translocation labels in one go or should I just add the one contrast I want to make and build a new …
- 105
1
vote
0
answers
394
views
vst() from DESeq2 vs voom() from limma
I have used both to transform my leukaemia RNA-Seq data for subsequent hierarchical clustering. The result is quite different. Some subtypes of leukaemia only form a cluster (or at least sit closer) i …
- 105
2
votes
2
answers
2k
views
TPM or rlog(CPM) for comparing expression?
While I can do a differential expression analysis with limma or DESeq2, I want to see how much each sample from my cohort expresses the gene. …
- 105