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deseq2 lowcount

updated 2.1 years ago by Michael Love 39k • written 8.1 years ago by aristotele_m ▴ 30

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Comment: How to extract proteins from PCs in plot_pca in DEP package by Basti ▴ 700

Which information do you want precisely ? plot_pca is just a wrapper for PCA visualization, but it applies prcomp to perform PCA : https://…

Comment: [limma::kegga] Pathway names all NA by Gordon Smyth 47k

The reason why installing limma didn't solve the problem was because you were using Bioconductor 3.15 rather than the current release, whic…

Comment: [limma::kegga] Pathway names all NA by andrewsm • 0

Thank you Gordon for the quick response. I saw something along those lines in the NEWS notes so did try ```{r} BiocManager:install("limma"…

Comment: Time-course, comparison of two groups by Gordon Smyth 47k

With 4 time points there are 3 df between time points, so your spline analysis with `df=3` is exactly the same as if you had treated time a…

Comment: Does DiffBind make consensus peaks sets for samples from a given condition (e.g. by tahir.msajid • 0

Hi Rory, I am normalizing the counts with the following options: `normalized <- dba.normalize(counts, method=DBA_DESEQ2, normalize = DBA_N…

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