User: anna_stavrinides

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Posts by anna_stavrinides

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Comment: C: Fisher test in Rna seq
... Hello, it's not clear from your question what it is you are testing with your fisher.test. Are you trying to test enrichment of the transcript in one condition versus another? If so it might be better to use a dedicated package for rna seq such as DESeq2 rather than fisher.test. I have used fisher. ...
written 4 months ago by anna_stavrinides20
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Comment: A: Timecourse Differential expression with multiple factors
... Hello again, Just an update on this question in case other readers find it helpful: I tried different methods for analysing my data, both grouping the samples in interesting ways, and also doing complicated contrasts to get the DEG in one go, but they all produced too many false positives. We noti ...
written 2.1 years ago by anna_stavrinides20
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Comment: C: Timecourse Differential expression with multiple factors
... Thank you very much for your detailed reply Aaron. I will try out the contrasts you mention and see if the results are cleaner than what I get with the contrasts I make. I had tried something similar after including a factor column to take into account the behaviour of the species:stage. (S for sen ...
written 2.1 years ago by anna_stavrinides20
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Comment: C: Timecourse Differential expression with multiple factors
... Thanks for the response Gavin, it has been helpful. I have tried approximating the contrasts by adding extra columns to take into account their behaviour but as you mention it is not very rigorous because the species are quite different expression-wise. I'll give it another go and see if I can't com ...
written 2.1 years ago by anna_stavrinides20
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Timecourse Differential expression with multiple factors
... Dear readers, I would greatly appreciate some help regarding analysis of a multi-factorial timecourse experiment, particularly regarding model selection and comparisons (either in edgeR or in DESeq2). My dataset consists of three closely related species sampled at three timepoints (3 reps for each ...
timecourse edger deseq2 written 2.2 years ago by anna_stavrinides20

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