Bioconductor Cydar

Showing : cydar • reset

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cydar

updated 5.5 years ago by Aaron Lun ★ 29k • written 5.5 years ago by thkapell ▴ 10

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Cydar CyTOF normalization

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by ghogg • 0

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cydar mass cytometry

updated 6.3 years ago by Aaron Lun ★ 29k • written 6.3 years ago by kenneth.baker • 0

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2.1k

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Cydar normalization normalizeBatch

updated 6.5 years ago by Aaron Lun ★ 29k • written 6.5 years ago by Florent ▴ 10

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1.4k

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cydar CyTOF

updated 6.7 years ago by Aaron Lun ★ 29k • written 6.7 years ago by mikhael.manurung ▴ 280

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1.2k

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cydar

8.3 years ago Lukas Weber • 0

6 results • Page 1 of 1

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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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