Bioconductor 2-dye

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limma 2-dye agilent common reference design

updated 9.3 years ago by James W. MacDonald 68k • written 9.3 years ago by Guido Hooiveld ★ 4.1k

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limma limma design matrix design and contrast matrix 2-dye

updated 9.4 years ago by Gordon Smyth 52k • written 9.4 years ago by Guido Hooiveld ★ 4.1k

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Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k

It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…

Answer: DESeq2 by ATpoint ★ 4.8k

Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …

Comment: Package developing and interoperation with Bioconductor by slizchap • 0

Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.

Comment: Package developing and interoperation with Bioconductor by slizchap • 0

Thank you so much for your answer, very useful!

Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Mike Smith ★ 6.6k

Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…

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Comment: ComBat with repeated measures

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