Bioconductor Deconvolution

Showing : Deconvolution • reset

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1.2k

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deconvolution r scRNAseq bioinformatics

2.2 years ago Hasan Alanya • 0

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1.0k

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deconvolution rnaseq psea

6.2 years ago WouterDeCoster ▴ 130

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897

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deconvolution methods

6.2 years ago casey.rimland ▴ 150

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1.1k

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deseq2 deconvolution rnaseq

updated 5.9 years ago by Michael Love 41k • written 5.9 years ago by jennyl.smith12 • 0

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1.3k

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deseq2 deconvolution normalization limma

updated 5.2 years ago by Michael Love 41k • written 5.2 years ago by bruce.moran ▴ 30

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732

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limma microarray deconvolution cell type

updated 4.2 years ago by Gordon Smyth 50k • written 4.2 years ago by antgomo • 0

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869

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methylCC deconvolution methylation dmrseq serum

4.0 years ago marcin.bazyliszek • 0

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651

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PSEA Deconvolution

3.9 years ago kavator ▴ 30

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1.6k

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deconvolution cellmix

8.9 years ago carleshf ▴ 10

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915

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Deconvolution

2.4 years ago Barista • 0

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2.2k

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deconvolution rna-seq

updated 8.6 years ago by Steve Lianoglou ★ 13k • written 8.6 years ago by Pauly Lin ▴ 150

11 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

Awards • All

Supporter to Jonathan ▴ 10