User: 183227851

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1832278510
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Posts by 183227851

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Comment: C: Deseq: What does "BaseMean" mean?
... Thanks! If a lot of differential taxa between compared groups were found by Deseq based on the microbiota data, is it necessary to set a cutoff for Basemean to keep more "prevalent" taxa as setting cutoffs for p value and FDR? If necessary, what is generally acceptable cuoff for Basemean? ...
written 7 weeks ago by 1832278510
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Comment: C: Deseq: What does "BaseMean" mean?
... Thanks! If a lot of differential taxa between compared groups were found by Deseq based on the microbiota data, is it necessary to set a cutoff for Basemean to keep more "prevalent" taxa as setting cutoffs for p value and FDR? If necessary, what is generally acceptable cuoff for Basemean? ...
written 7 weeks ago by 1832278510
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Deseq: What does "BaseMean" mean?
... Deseq: What does BaseMean (output of deseq) mean? I cannot find its description in the manual. ...
deseq2 written 7 weeks ago by 1832278510 • updated 7 weeks ago by Guido Hooiveld2.3k
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Comment: C: edgeR - how to build design for matched case-control study with repeated measure
... Thank you very much! For the 1st question, actually, the extra variables such as smoking may correlate with disease (these variables are not confounded with matchid), thus we want to obtain a pure correlation between microbiome and disease by adjusting these variables (For example, in multivariate ...
written 4 months ago by 1832278510
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Comment: C: edgeR - how to build design for matched case-control study with repeated measure
... Thanks a lot for your professional and quick reply!! I appreciate it very much. There are 3 more questions: 1) If I need to adjust for some confounding factors such as smoking and drinking. Can I just add these variables into the model.matrix? Like design <- model.matrix(~matchid + time +smoking ...
written 4 months ago by 1832278510
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Comment: C: DESeq2 - how to build design for matched case-control study with repeated measur
... OK! Thanks! ...
written 4 months ago by 1832278510
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edgeR - how to build design for matched case-control study with repeated measurement
... Please help me build a design that accounts for both the matched case-control design (there were 1 case [disease=1] and 2 controls [disease=0] in each pair [having the same matchid], matched for age and gender) and the correlation between multiple measurements at different timepoints (time 1, 2, 3) ...
edger written 4 months ago by 1832278510 • updated 4 months ago by Aaron Lun21k
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Comment: C: DESeq2 - how to build design for matched case-control study with repeated measur
... Thanks Michael! Compared to limma, I am more familiar with edgeR. EdgeR can also compare the microbial differential abundance between cases and controls. Additionally, there are a lot of examples in the edgeRUsersGuide. If I use edgeR, is the design correct? design <- model.matrix(~matchid+perso ...
written 4 months ago by 1832278510
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Comment: C: DESeq2 - how to build design for matched case-control study with repeated measur
... Many thanks for your professional and quick reply. If I want to stick to DESeq2 and I only want to account for correlation between multiple measurements at different timepoints (time 1, 2, 3) in a given subject(ignoring the matching for the moment),how should I build the design.My objective is to co ...
written 4 months ago by 1832278510
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DESeq2 - how to build design for matched case-control study with repeated measurement
... Please help me build a design that accounts for both the matched case-control design (there were 1 case [disease=1] and 2 controls [disease=0] in each pair [having the same matchid], matched for age and gender) and the correlation between multiple measurements at different timepoints (time 1, 2, 3) ...
deseq2 written 4 months ago by 1832278510 • updated 4 months ago by Michael Love20k

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