User: Papyrus
Papyrus • 10
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Posts by Papyrus
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... I would certainly add the [limma][1] package, which contains functionality for several gene set enrichment tests (roast, camera, romer).
And also [goseq][2], to perform the simpler over-representation analyses
[1]: http://bioconductor.org/packages/release/bioc/html/limma.html "limma"
[2]: ...
written 6 days ago by
Papyrus • 10
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... I'm using M-values as recommended because they're more gaussian. Indeed, I was looking at PCA before and after adjustment to see how the variance was shrinking in some dimensions related or not to known variables.
Regarding the use of the coefficients before the differential I think I will incorpor ...
written 9 weeks ago by
Papyrus • 10
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... I'm using limma for the tests and such.
Yes, that's *exactly* what I was trying to observe: see If I got the same results from limma from doing:
**Y ~ tumor/control + sva1 + sva2**
Versus doing the model with Y and tumor/control pre-adjusted for the linear influence of the SVAs: ** Y.adj ~ tumor/c ...
written 10 weeks ago by
Papyrus • 10
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... Thanks for the detailed and thorough response.
Yes, I think my confusion relates to what you say here: "*However, batch effect correction for visualization is different from using batch SV residuals as factors for differential analysis*".
In my case I was playing with a linear model:
**Y ~ tumor ...
written 10 weeks ago by
Papyrus • 10
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... Hi ivivek_ngs:
I've used your function and found that it gives the same result as obtaining the residuals from this linear model:
Y ~ SVs
However: I think maybe this solution doesn't take into account the influence of SVs on our variable of interest?
For example, I found in this paper: ht ...
written 11 weeks ago by
Papyrus • 10
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