## User: tleona3

tleona30
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1 year, 6 months ago
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#### Posts by tleona3

<prev • 6 results • page 1 of 1 • next >
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... 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 18 hours ago by tleona30
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... 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 18 hours ago by tleona30
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... 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 ...
written 10 days ago by tleona30 • updated 10 days ago by Gordon Smyth36k
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... 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 17 days ago by tleona30
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... 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 18 days ago by tleona30
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... 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 ...
written 20 days ago by tleona30 • updated 19 days ago by Aaron Lun22k

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