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1.9k

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contrast limma

updated 10.1 years ago by Gordon Smyth 53k • written 10.1 years ago by John linux-user ▴ 210

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5.4k

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deseq2 padj contrast results

updated 10.2 years ago by Michael Love 43k • written 10.2 years ago by jjinhyoungkim ▴ 20

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5.3k

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deseq2 heterosis contrast design and contrast matrix

updated 10.3 years ago by Michael Love 43k • written 10.3 years ago by johntlovell ▴ 10

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3.5k

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deseq2 interactions contrast

10.4 years ago shao ▴ 100

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3.9k

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limma voom contrast

updated 10.6 years ago by Steve Lianoglou ★ 13k • written 10.6 years ago by Stijn van Dongen ▴ 80

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12k

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deseq2 multiple factor design contrast interactions

updated 10.7 years ago by Michael Love 43k • written 10.7 years ago by mat.lesche ▴ 110

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3.8k

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deseq2 contrast design

updated 10.8 years ago by Michael Love 43k • written 10.8 years ago by ksilkaitis • 0

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4.9k

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limma contrast design and contrast matrix

11.0 years ago • updated 10.9 years ago Smith H. ▴ 20

58 results • Page 2 of 2

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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…

Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20

thank you so much for answering Dr. Love!

Answer: DESeq2 for candidate gene analysis by Michael Love 43k

Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…

Votes

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

DESeq2 for candidate gene analysis

Answer: DESeq2 for candidate gene analysis

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