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DESeq2 log2FC vst()

updated 3 months ago by ATpoint ★ 4.4k • written 3 months ago by lifeonmars • 0

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Answer: Which input data is acceptable for MAST? by Andrew_McDavid ▴ 270

Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…

Answer: segfault when using singleR with Azimuth reference by James W. MacDonald 67k

The training step is usually faster than the classification step, so you might try running `trainSingleR` on the reference to see if that i…

Comment: Batch Effect in DESeq2, how to control, how to remove it, how to address biologi by James W. MacDonald 67k

You don't. I believe Fisher has a quote that applies here. Also, please don't add to five year old posts. Start a new one.

Comment: Convert HGVS Representation back to Reference Genome Coordinates by Vince Schulz ▴ 160

Not a bioconductor solution, and probably not easily code-able, but there is a batch validate/convert function available here: https://vari…

Answer: How to control batch effect if Group and batch are same? by ATpoint ★ 4.4k

You cannot do any correction. That's the simple and only answer. You cannot distinguish true biological effect from unwanted technical vari…

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Comment: Normalization RNA-seq for multiple plates

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