Bioconductor TCGAutils

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TCGAutils

updated 4 months ago by James W. MacDonald 68k • written 4 months ago by xiaofeiwang18266 ▴ 60

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normalization RNASEQ Normalization TCGAutils TCGA

updated 2.5 years ago by ATpoint ★ 4.8k • written 2.5 years ago by Deniz • 0

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MultiAssayExperiment curatedTCGAData TCGAutils

4.4 years ago svlachavas ▴ 840

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1.6k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.5 years ago by Marcel Ramos 700 • written 4.5 years ago by svlachavas ▴ 840

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 4.5 years ago by Marcel Ramos 700 • written 4.6 years ago by svlachavas ▴ 840

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 5.8 years ago by Marcel Ramos 700 • written 5.9 years ago by Dario Strbenac ★ 1.6k

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960

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TCGAutils

updated 6.1 years ago by Levi Waldron ★ 1.1k • written 6.1 years ago by vittorio.fortino • 0

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TCGAutils multiassayexperiment coad

updated 6.9 years ago by Marcel Ramos 700 • written 6.9 years ago by mario.zanfardino ▴ 160

8 results • Page 1 of 1

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Comment: Limma trend with limpa by Alejandro • 0

Dear Gordon, Thank you very much!

Answer: DESeq2 from phyloseq error by asafpr • 0

Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …

Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0

Thank you for your reply! There are some pretty big discrepancies in the total raw counts between samples: ![enter image description here…

Answer: Limma trend with limpa by Gordon Smyth 52k

Dear Alejandro, Thanks for your interest. No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …

Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k

Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…

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Comment: Check removeBatchEffect effectiveness

Answer: Check removeBatchEffect effectiveness

A: what should I do with many zero counts from Salmon quantification

Comment: parameters of filterByExpr

GAlignments Cigar to GRanges

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