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limma dose-response lincs tempO-seq high-throughput transcriptomics

updated 7.0 years ago by Gordon Smyth 51k • written 7.0 years ago by Pekka Kohonen ▴ 190

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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 ▴ 150

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…

Comment: Batch Effect in DESeq2, how to control, how to remove it, how to address biologi by Bioinformagician • 0

How to control batch effect if Group and batch are same?. For example, I have all tumor samples from batch1 and all normal samples from bat…

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Answer: Deseq2 sfType

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