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question about normalization of RNAseq by tweeDEseq using TMM from edgeR
Normalization edgeR tweeDEseq Normalization edgeR tweeDEseq
updated 10.3 years ago by ★ 2.8k • written 10.3 years ago by ▴ 90
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Run tweeDEseq on Flux-capacitor RPKM values
tweedeseq differential expression
updated 4.3 years ago by ★ 2.8k • written 4.3 years ago by • 0
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tweeDEseq glm reduced model specification?
tweeDEseq tweeDEseq
updated 8.7 years ago by ▴ 20 • written 8.7 years ago by 7.8k
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tweeDEseq main paper
edgeR tweeDEseq edgeR tweeDEseq
8.7 years ago Gonzalez Ruiz, Juan Ramon ▴ 20
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Creating model for DE analysis in tweeDEglm
tweedeseq
7.0 years ago keever1 • 0
5 results • Page 1 of 1
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Comment: edgeR: the F-statistics changed after removing lowly expressed gene by Gordon Smyth 45k
There is nothing to be gained by doing analyses without filtering. We don't recommend it.
Comment: edgeR: the F-statistics changed after removing lowly expressed gene by Pei • 0
Thank you Prof. Smyth! In my case, I found that number of significant genes tend to decrease after filtering when using glmQLFTest but num…
Answer: edgeR: the F-statistics changed after removing lowly expressed gene by Gordon Smyth 45k
glmQLFTest() function is designed to be used after expression filtering. You should apply expression filtering, regardless of whether it re…
Comment: EnrichGO not working with db created from annotationhub by Lucía • 0
I have this, can this be used for GO in R? ``` 115709282 LOC115709282 phenylalanine ammonia-lyase 115699364 LOC115699364 …
Answer: EnrichGO not working with db created from annotationhub by Lucía • 0
Hi, thanks so much for all your replies and running the code and confirming. I have not seen any GO term annotations for Cannabis so far…
Votes
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
Answer: Difference between raw counts and featureCounts for DESeq2
A: Differential expression of RNA-seq data using limma and voom()
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Teacher to Gordon Smyth 45k
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Scholar to James W. MacDonald 59k
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