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282

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rna-seq edgeR

updated 3 days ago by Gordon Smyth 50k • written 16 days ago by Netanel • 0

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7.8k

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deseq2 edgeR rna-seq

updated 6 days ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

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DGEList edgeR

5 days ago prity6459 • 0

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126

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subsettingdata edgeR designmatrix

updated 5 days ago by Gordon Smyth 50k • written 6 days ago by prity6459 • 0

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1.5k

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salmon edgeR tximport nf-core gene_counts

updated 5 days ago by i.atanasoai • 0 • written 14 months ago by mohammedtoufiq91 ▴ 10

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322

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edgeR

7 days ago • updated 2 days ago Jonathan ▴ 10

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edgeR

updated 1 day ago by Gordon Smyth 50k • written 1 day ago by k___ ▴ 30

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112

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limma edgeR RNASeq

updated 5 days ago by Gordon Smyth 50k • written 6 days ago by Shaimaa Gamal • 0

8 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

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