User: 13530213

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1353021310
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Posts by 13530213

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Answer: C: Differences between PCA plots in DESeq and FactoMineR
... Hi there, So, unfortunately I cannot see the plots and therefore not discuss them. However, there is a possibility that the PCA analysis was not centered and was in the other, or was scaled in one but not the other. I generally do center, but not scale my PCA analysis. Other then that, I should read ...
written 4 days ago by 1353021310
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Comment: C: EdgeR and contrasts: How to compare with a group not in the model
... Ok, so... Making a design and then comparing COEFs is probably the hardest thing in EdgeR or DE in general. Up to now. I changed my code slightly; design <- model.matrix(~0 + Group + Gender + Age, data = master.table) This makes it so that the design has all the groups that I want to compar ...
written 6 weeks ago by 1353021310
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Comment: C: EdgeR and contrasts: How to compare with a group not in the model
... Hey @h.mon, thanks for the reply. Is it correct that if I only have GroupM and GroupS, that just filling in GroupM or GroupS would be a comparison of the group agains baseline (groupC) ? ...
written 6 weeks ago by 1353021310
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EdgeR and contrasts: How to compare with a group not in the model
... Hi all, I am struggling to make a contrast with EdgeR. design <- model.matrix(~Gender + Age + Group, data = patient.table) The (disease) Group is a factor with [Control, Mild, Severe]. I want to compare C-M. M-S and C-S. Thus s i DGEL <- edgeR::DGEList(expressionData) keep <- ...
R makecontrasts model.matrix rna-seq edger written 6 weeks ago by 1353021310

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Scholar 4 days ago, created an answer that has been accepted. For C: Differences between PCA plots in DESeq and FactoMineR

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