Bioconductor Lfcthreshold

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923

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DESeq2 lfcThreshold

15 months ago Abir.khazaal ▴ 10

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1.3k

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lfcshrink DESeq2 RNASeq lfcthreshold

17 months ago ClaudiaE • 0

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1.7k

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ashr Deseq2 lfcThreshold

updated 2.2 years ago by Michael Love 41k • written 3.6 years ago by Iryna • 0

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6.5k

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deseq2 differential expression logfoldchange lfcshrink lfcthreshold

updated 2.5 years ago by Michael Love 41k • written 5.5 years ago by emi.sch ▴ 20

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933

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deseq2 lfcshrink lfcthreshold differential gene expression

updated 5.0 years ago by Michael Love 41k • written 5.0 years ago by corentinrichard374369 • 0

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2.0k

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DESeq2 lfcThreshold

updated 5.7 years ago by Michael Love 41k • written 5.7 years ago by Mike ▴ 10

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4.9k

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lfcthreshold deseq2

updated 5.9 years ago by Michael Love 41k • written 6.0 years ago by lirongrossmann ▴ 80

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2.9k

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deseq2 microrna lfcThreshold stable expression ffpe

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by mariakarand ▴ 20

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Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0

Thank you for your response Gordon :) I've already run the code below, just add batch to the limma linear model design <- model.matri…

Answer: Correct the batch effect in methylation analysis in R by Gordon Smyth 49k

You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model. …

Answer: Agilent Microarray Gene Oncology analysis gone wrong by Gordon Smyth 49k

Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…

Comment: Normalised counts from RUVg in RUVSeq by Shaimaa Gamal • 0

Hello I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …

Comment: enrichGOgradient color change by James W. MacDonald 64k

You could look at my answer and extrapolate from there.

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Answer: Correct the batch effect in methylation analysis in R

Answer: enrichGOgradient color change

Answer: Filter genes by expression for voomLmFit

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