Bioconductor FoldChange

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1.7k

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limma RNAseq foldchange

6.1 years ago • updated 6.0 years ago susana.amaral.teixeira ▴ 20

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1.8k

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limma microarray foldchange DEG GEO

updated 5.1 years ago by Gordon Smyth 52k • written 5.1 years ago by Pietro ▴ 40

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1.4k

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FoldChange DiffBind lfcShrink Cut&TagData

21 months ago bhandary.8590 ▴ 20

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6.8k

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DifferentialExpression DEA FC FoldChange edgeR

3.5 years ago zhxiaokang ▴ 20

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3.0k

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EdgeR RNAseq Foldchange

updated 3.7 years ago by swbarnes2 ★ 1.4k • written 3.7 years ago by najib • 0

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1.6k

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DEXSeq DTU salmon rnaseqDTU foldchange

updated 5.9 years ago by Michael Love 43k • written 6.2 years ago by fiona.dick91 ▴ 60

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971

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StatisticalMethod FoldChange edgeR RNASeq

15 months ago Sabiha ▴ 20

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4.9k

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FoldChange DiffBind lfcShrink

updated 20 months ago by Rory Stark ★ 5.2k • written 20 months ago by bhandary.8590 ▴ 20

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1.5k

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sign FoldChange DESeq2 reference

updated 3.2 years ago by Michael Love 43k • written 3.2 years ago by yampolsk • 0

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1.2k

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edgeR RNA-Seq log2 foldchange q_value

updated 3.2 years ago by Gordon Smyth 52k • written 3.2 years ago by johndavidgriner74 • 0

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2.1k

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DESeq2 TPM Foldchange

updated 3.0 years ago by Michael Love 43k • written 3.0 years ago by dadca596 • 0

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3.8k

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foldchange topGO DifferentialExpression enrichment

updated 4.4 years ago by Gordon Smyth 52k • written 4.4 years ago by lessismore ▴ 20

12 results • Page 1 of 1

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Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…

Comment: GAGE kegg.gsets() self-signed certificate error by Lucas • 0

Hello, I ended up solving the issue by using the first strategy: Disable the SSL certificate Verification. I used the following code to …

Comment: Clarification on GOALL / GO2ALLORFs mapping by DavideSant • 0

Thank you for your answer James. I have to disagree though, at the SGD webpage you posted there is no indication that "GO:0045719 - negati…

Comment: Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Ana by Michael Love 43k

And to add to this: when you put a generic package (e.g. DESeq2) as a tag, it actually emails the maintainer.

Answer: Using TPM from tximport of Salmon output for singscore by Michael Love 43k

TPM is fine, I've also sometimes used TPM with some robust column scaling, e.g.: ``` sf <- DESeq2::estimateSizeFactorsForMatrix(txi$abu…

Votes

Answer: Using TPM from tximport of Salmon output for singscore

Comment: Using TPM from tximport of Salmon output for singscore

Answer: affy::rma results doesn't match with ncbi website

Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types

Answer: Replicates in DESeq2

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