Bioconductor ShRNAseq

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shrnaseq edger experimental design model.matrix

updated 6.9 years ago by Aaron Lun ★ 29k • written 6.9 years ago by Assa Yeroslaviz ★ 1.5k

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shRNAseq edgeR shRNA

updated 10.1 years ago by Gordon Smyth 53k • written 10.1 years ago by KB ▴ 50

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Comment: Help with defining groups by Phinney, Brett ▴ 10

I got it working , thank you!!!

Comment: Check removeBatchEffect effectiveness by massimo • 0

I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…

Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0

Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.

Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k

Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…

Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k

Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…

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Comment: Check removeBatchEffect effectiveness

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