User: tleona3

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tleona30
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Posts by tleona3

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Comment: C: LIMMA dupcor() function time issue.
... I randomly chose 10,000 rows 1,000 times from the entire dataset (since it was ordered in a specific way) to run the `duplicateCorrelation` function and got a normally distributed `corfit$consensus` so I used the median value as my parameter for my actual experiment. Thanks for all the help! ...
written 8 months ago by tleona30
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Comment: C: LIMMA time series spline model.matrix design setup
... For the results output from the following contrast listed (also above): con.6 <- makeContrasts((M6 - M0) - (C6 - C0), levels=design) res <- topTable(both.fit2, coef = "con.6", number = Inf, adjust.method = "BH") In this results file, do the positive test statistics correspond to gene ...
written 8 months ago by tleona30
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LIMMA dupcor() function time issue.
... I am trying to apply the LIMMA package to a dataset that is much larger than a traditional microarray or RNA-seq experiment. The number of samples is 96, but the number of observations is ~11,127,676. I have been able to run LIMMA on this dataset previously to make different comparisons between samp ...
microarray limma block written 8 months ago by tleona30 • updated 8 months ago by Gordon Smyth39k
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Comment: C: LIMMA time series spline model.matrix design setup
... Just to clarify, con.6 <- makeContrasts((M6 - M0) - (C6 - C0), levels=design) This tests the null hypothesis that the 6 hour response is the same (not different) between tissues. The alternative hypothesis is that they are not the same, correct? ...
written 8 months ago by tleona30
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Comment: C: LIMMA time series spline model.matrix design setup
... Hi Aaron, this is all great information and I really appreciate you taking the time to help! This particular step was a current bottleneck in my project as I wanted to get it right and I'm excited to move forward with it. ...
written 8 months ago by tleona30
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LIMMA time series spline model.matrix design setup
... I have reviewed the LIMMA manual (esp. sections 9.6.1 and 9.6.2), and need conceptual help in applying either this approach to my experimental design or suggestions to use an alternative approach. My microarray RNA data is as follows: Two tissue types, five time points (0, 6, 24, 72, 168 hours), ~2 ...
limma design model.matrix time series splines written 8 months ago by tleona30 • updated 8 months ago by Aaron Lun25k

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