Bioconductor SmallRNA

Showing : SmallRNA • reset

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smallrna counts

7.6 years ago ribioinfo ▴ 100

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TMM deseq2 smallrna rnaseq

updated 5.4 years ago by António Miguel de Jesus Domingues ▴ 490 • written 5.4 years ago by Konstantinos Yeles ▴ 80

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Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR

updated 11.6 years ago by Steve Lianoglou ★ 13k • written 11.6 years ago by Weng Khong LIM ▴ 10

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Sequencing SmallRNA Microarray limma Sequencing SmallRNA Microarray limma

updated 9.7 years ago by James W. MacDonald 65k • written 9.7 years ago by Jakub Stanislaw Nowak ▴ 70

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Sequencing miRNA SmallRNA DESeq Sequencing miRNA SmallRNA DESeq

updated 13.4 years ago by Wolfgang Huber ★ 13k • written 13.4 years ago by Wu, Xiwei ▴ 350

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Sequencing SmallRNA edgeR Sequencing SmallRNA edgeR

updated 11.6 years ago by Mark Robinson ▴ 880 • written 11.6 years ago by Danie ▴ 40

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915

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counts SmallRNA Normalization

updated 2.4 years ago by hauken_heyken ▴ 80 • written 2.5 years ago by k___ ▴ 30

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684

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SmallRNA DESeq2

21 months ago • updated 20 months ago jucosie • 0

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655

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DESeq2 SmallRNA

updated 8 weeks ago by Michael Love 41k • written 8 weeks ago by r.r.bioinf • 0

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matrix DESeq2 SmallRNA dimensions small

2.6 years ago andreia ▴ 10

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mirna riboseq smallrna differential gene expression Job

6.1 years ago Andy Lynch ▴ 120

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cancer sequencing rnaseq methylation smallrna Job

5.8 years ago Andy Lynch ▴ 120

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deseq2 normalization smallrna ribosomal rna

7.5 years ago mosharrofgeb ▴ 10

13 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