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Comment: Sva and batch effect
by
Gordon Smyth
47k
(+1). I find that ComBat tends to introduce spurious differential expression so, you think there's a batch effect affecting the variances a…
Comment: Advice for the analysis of microarray data with limma
by
Gordon Smyth
47k
You mean references on orthogonal polynomials? Polynomial approximation is a classic topic in mathematics and statistics and there are many…
Comment: Limma-voom with inverse probability weights (similar to sample weights)
by
Gordon Smyth
47k
The potential problem isn't with empirical Bayes with the fact that the variance estimate from your method A linear model might not be mean…
Answer: Sva and batch effect
by
James W. MacDonald
62k
You shouldn't be computing regular t-statistics to begin with. In addition, `sva` is intended to adjust for *unobserved variability*, and a…
Answer: Micro Array GEO data analysis
by
James W. MacDonald
62k
You could try getting the RCC files and normalizing yourself, using `getGEOSuppFiles` and the `NanoStringNorm` package. Or just use NanoStr…
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