Bioconductor StandR

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stand standR

7 hours ago • updated 20 minutes ago joseph.joonsang • 0

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SummarizedExperiment StandR

updated 21 months ago by helucro ▴ 70 • written 21 months ago by MxT • 0

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Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0

> dim(spe) [1] 19962 425

Comment: fail to use addPerROIQC in Rmd by liu.n • 0

Hi, what's the output from `dim(spe)`?

Answer: DESeq2- merging technical vs biological replicates by Michael Love 43k

Technical replicates (more sequencing of same library) you can use `collapseReplicates()`. But biological replicates are best handled wi…

Answer: lfcShrink and alpha value by Michael Love 43k

`summary()` is just printing a particular `alpha`, but you can do: ``` summary(res, alpha = ...) ```

Answer: DESeq2 dispersion estimates fitting drastically different based on explanatory v by Michael Love 43k

> DESeq2 treats this as a numeric variable with a range from 19560-19660 And it gives a warning to not use this type of covariate, which…

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