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2

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limma fit design RNASeq edgeR

9 months ago Sabiha ▴ 20

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5

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rnaseq linear model fit deseq2

updated 7.6 years ago by Michael Love 43k • written 7.6 years ago by lina.faller ▴ 10

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dexseq fit matrix warning

updated 3.1 years ago by koushik • 0 • written 7.9 years ago by Assa Yeroslaviz ★ 1.5k

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7

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limma goodness fit linear model

updated 10.0 years ago by Gordon Smyth 52k • written 10.0 years ago by nonCodingGene ▴ 10

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Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k

The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…

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…

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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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