User: gstone2
gstone2 • 0
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Posts by gstone2
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... I am implementing the design you've recommended and am concerned that I am not getting the contrast I am interested in. The columns Male.post and Female.post in my design matrix have a 1 for all male and female samples, respectively, taken post condition. When I contrast these, Female.post-Male.post ...
written 12 months ago by
gstone2 • 0
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... Thank you for all the help!
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written 12 months ago by
gstone2 • 0
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... Thank you for your elaboration--it's made me think much more. I am looking at the change in gene expression due to condition within each sex and between the sexes (f.post-f.pre)-(m.post-m.pre), so I am comparing across patients. I get the sense from your explanation that it doesn't hurt to add the c ...
written 12 months ago by
gstone2 • 0
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... Thank you for the great explanation!
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written 12 months ago by
gstone2 • 0
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... I have received extraordinary help on this website, and while I have learned a lot about limma, I am still a beginner and am trying to overcome certain limitations. I am trying to determine the effect of a condition within and between the sexes, and one limitation is that I do not feel comfortable i ...
written 12 months ago by
gstone2 • 0
• updated 12 months ago by
Ryan C. Thompson ♦ 6.5k
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... Ok great. Thank you very much for all of your help!
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written 12 months ago by
gstone2 • 0
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... Ok thank you, that makes a lot of sense. So just that I am clear, in both cases, sexMale_conditionpost represents the log-fold change from pre to post in males?
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written 12 months ago by
gstone2 • 0
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... So in the case when my design matrix is ~ patient + sex:condition, I should remove the pre terms from the design and then construct my contrast matrix: makeContrasts(sexDiff = "sexFemale_conditionpost - sexMale_conditionpost", levels=design)
Now, in the case when my design matrix is ~ 0 + patient + ...
written 12 months ago by
gstone2 • 0
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... Great, thank you. Yes, nested is a factor. However, since I have an uneven amount of males and females it is my understanding that I should remove columns from the design matrix that do not correspond to a sample. Am I correct in thinking this?
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written 14 months ago by
gstone2 • 0
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... I apologize, I am answering from a different account since I seem to have reached a positing limit. Nested is numbering each sample within its sex group, as recommended by the edgeR manual in the section detailing making comparisons between and within groups.
I would like to use limma to contrast t ...
written 14 months ago by
gstone2 • 0
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