Bioconductor Cytof

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910

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cydar CyTOF

updated 5.2 years ago by Aaron Lun ★ 28k • written 5.2 years ago by mikhael.manurung ▴ 270

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1.3k

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cytofkit cytof write.csv output

updated 7.5 years ago by chen_hao ▴ 30 • written 7.5 years ago by cjackson13 • 0

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2.7k

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flowCore flowcore CyToF Rtsne

updated 8.7 years ago by Jiang, Mike ★ 1.3k • written 8.7 years ago by clevy ▴ 10

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1.6k

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Cydar CyTOF normalization

updated 4.6 years ago by Aaron Lun ★ 28k • written 4.6 years ago by ghogg • 0

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1.0k

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deseq2 mass cytometry CyTOF

updated 3.6 years ago by Michael Love 41k • written 3.6 years ago by mikhael.manurung ▴ 270

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623

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batch effect cytof

4.1 years ago mikhael.manurung ▴ 270

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1.4k

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Cytofast FlowSom CyTOF fcs files

3.5 years ago domenico.somma • 0

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709

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cytofWorkflow cytof diffcyt

3.3 years ago achaillon • 0

8 results • Page 1 of 1

Recent ...

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0