User: Loodramon

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Loodramon0
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Posts by Loodramon

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Comment: C: LIMMA for paired analysis with adjustment for confounding continuous variables
... Yes I agree that the within patient group can't be confounded as obviously its the same patients but the confounding concern is for the between group response comparison given by the contrast: con.t1vt2<-makeContrasts(((t1wk24-t1wk0)-(t2wk24-t2wk0)), levels=design) Also agree regarding includin ...
written 3.7 years ago by Loodramon0
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Comment: C: LIMMA for paired analysis with adjustment for confounding continuous variables
... The goal of including the values of the baseline clinical variables that show between group differences is more to control for effects similar to regression to the mean. I.e. If the expression of a gene increased in one of the groups but not the others and that group which had the increase had the h ...
written 3.7 years ago by Loodramon0
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Answer: A: LIMMA for paired analysis with adjustment for confounding continuous variables
... Thanks for your answer Aaron. Yes what you've suggested is pretty much my 'unadjusted' model. However, because there are differences at baseline between the two groups in the confounding variables I wanted to include them in the model to account for DE genes in the direct between group compariso ...
written 3.7 years ago by Loodramon0
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Comment: C: LIMMA for paired analysis with adjustment for confounding continuous variables
... It's a vector containing the Patient IDs as factors. There's 12 patients with 2 arrays each. You'll notice that the confound1 values repeat at array 13, this is the start of the wk24 arrays. ...
written 3.7 years ago by Loodramon0
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LIMMA for paired analysis with adjustment for confounding continuous variables
... Hi, I'm analysing a longitudinal gene expression qPCR array study in LIMMA. I have 2 groups with baseline and week 24 measurements. I also have 2 confounding baseline continuous variables that I would like to include in the model. I found something similar discussed here: https://stat.ethz.ch/pipe ...
limma paired confounding adjustment gene expression written 3.7 years ago by Loodramon0

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