Bioconductor Ruvr

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rnaseq ruvseq RUVr edgeR

9.0 years ago David R ▴ 90

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RUV ruvseq ruvr ruvnormalize single cell

7.3 years ago Nik Tuzov ▴ 90

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edger RUVseq RUVr GLM RNAseq

5.5 years ago garbuzov • 0

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Answer: lfcShrink and alpha value by Michael Love 43k

The code I sent just tells summary what threshold to use when printing the table.

Comment: Crossover design with limma by Marek Gierlinski ▴ 30

Thank you for your answer. It is an interesting solution. I've never though of modifying the design matrix itself - I always try to have a …

Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k

According to the the help page of `pathview` (type `?pathview`) the input should be `either vector (single sample) or a matrix-like data (m…

Comment: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You can examine the structure of a `DelayedMatrix` by calling the `showtree()` function. For example: ``` library(scRNAseq) X <- fetchData…

Comment: lfcShrink and alpha value by cropero • 0

Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…

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Answer: Crossover design with limma

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