User: microbe

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Posts by microbe

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Comment: C: DESeq2: Is it possible to have incomplete pairs of samples?
... Dear Michael, I now understand the point I was missing! Thanks for making it clear to me the reason why keeping unpaired samples would not make any difference in the current design. Please allow me ask one last question: Because my sample size is quite limited, I am thinking of dropping the pair ...
written 10 days ago by microbe0
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Comment: C: DESeq2: Is it possible to have incomplete pairs of samples?
... Dear Michael, Thank you for your reply! Please correct me if I missed something, but duplicateCorrelation() is a function in limma and I need to work with DESeq2 for the time being for various reasons. If it is not acceptable to keep the unpaired sample in my dataset with "design ~ ParticipantID ...
written 10 days ago by microbe0
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Comment: C: DESeq2: Is it possible to have incomplete pairs of samples?
... Dear James, Thank you for your reply and sorry for my question being unclear. What I should have asked was "if I have an unpaired sample, would the other paired samples still be tested for the effect of treatment (the second factor, i.e. "Group") and be controlled for the effect of participant (t ...
written 11 days ago by microbe0
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DESeq2: Is it possible to have incomplete pairs of samples?
... To the developers of DESeq2, First of all, thank you for creating such a great tool! I am currently trying to analyze 16S rRNA gene amplicon sequencing data of samples which were taken from the oral microbiota of patients at two timepoints: before and after treatment. My colData is as below: `` ...
deseq2 written 11 days ago by microbe0 • updated 11 days ago by James W. MacDonald52k

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