Bioconductor Significance

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deseq2 betaPrior shrinkage significance

6.7 years ago brynedal ▴ 40

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1.9k

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dna methylation illimina 450k methylation beta M significance

updated 7.3 years ago by James W. MacDonald 67k • written 7.3 years ago by skids121 • 0

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1.2k

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limma edger significance rnaseq

updated 7.9 years ago by Gordon Smyth 52k • written 7.9 years ago by roberto.spreafico ▴ 20

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1.5k

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salmon transcripts significance counts

8.5 years ago Assa Yeroslaviz ★ 1.5k

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2.9k

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deseq2 wald lrt genes significance

updated 8.6 years ago by Michael Love 43k • written 8.6 years ago by aziza ▴ 20

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1.0k

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cellcode significance

8.7 years ago christopher.clarskon15 ▴ 20

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Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0

Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…

Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k

I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…

Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…

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Answer: How do I fix an odd voom plot in a combined dataset?

Comment: How do I fix an odd voom plot in a combined dataset?

C: How does edgeR cpm function calculate log(CPM) values?

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