Bioconductor Warnings

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rna-seq deseq2 warnings nbinomWaldTest transformation

updated 2.9 years ago by Michael Love 40k • written 2.9 years ago by andreia ▴ 10

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limma batchcorrect warnings

updated 4.2 years ago by Aaron Lun ★ 28k • written 4.2 years ago by xingxd16 ▴ 20

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cmd check warnings s3

updated 6.8 years ago by Gordon Smyth 47k • written 6.8 years ago by anthonycolombo60 • 0

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DEXSeq warnings dexseq_count

updated 7.1 years ago by Darya Vanichkina ▴ 120 • written 7.1 years ago by Assa Yeroslaviz ★ 1.5k

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warnings gostats

updated 8.1 years ago by James W. MacDonald 63k • written 8.1 years ago by jon.young • 0

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software error warnings synapter

8.5 years ago sogueta • 0

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Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k

PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would to the job.

Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k

> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …

Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0

Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.

Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10

@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…

Comment: WGCNA: many over and under-expressed features in modules of a signed network by andres.firrincieli ▴ 50

answered in Biostars: https://www.biostars.org/p/9564943/

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Answer: Question on constructing design matrix and defining contrasts for analysis

WGCNA: many over and under-expressed features in modules of a signed network

Comment: WGCNA: many over and under-expressed features in modules of a signed network

Answer: DESeq2 or edgeR for Presence and Absence of Proteins

Answer: Normalized counts from LRT or Wald test?

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Teacher to James W. MacDonald 63k