Bioconductor Replicates

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conditions replicates SmallRNAData DESeq2

updated 3 months ago by Kevin Blighe ★ 3.9k • written 4 months ago by samer ▴ 10

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629

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DESeq2 timecoursedata replicates

updated 13 months ago by Michael Love 41k • written 14 months ago by fepesanz8 • 0

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2.6k

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deseq2 R bioconductor RNA_Seq replicates

updated 4.4 years ago by swbarnes2 ★ 1.3k • written 4.4 years ago by aishu.jp ▴ 30

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1.8k

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rnaseq deseq2 differential expression batch effect replicates

updated 4.6 years ago by Michael Love 41k • written 4.6 years ago by Nik dAK ▴ 10

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3.2k

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deseq2 replicates error DESeqDataSetFromMatrix

updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by Yonatan Amzaleg • 0

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2.8k

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limma proteomics replicates

updated 5.7 years ago by Aaron Lun ★ 28k • written 5.7 years ago by ivansilbern • 0

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2.0k

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limma duplicatecorrelation replicates

7.0 years ago rwalke13 • 0

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1.6k

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deseq2 replicates

updated 7.2 years ago by Michael Love 41k • written 7.2 years ago by le2336 ▴ 20

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5.1k

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DESEQ deseq2 deseq replicates biologicalreplicates

8.4 years ago wd ▴ 30

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1.2k

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rnbeads replicates

updated 8.4 years ago by rnbeads • 0 • written 8.5 years ago by Jon Manning ▴ 40

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891

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replicates

8.7 years ago efratdahan21 • 0

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2.3k

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edgeR rna-seq replicates

updated 9.2 years ago by James W. MacDonald 65k • written 9.2 years ago by eb0906 • 0

12 results • Page 1 of 1

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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.

Comment: 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…

Comment: get BM error by Fara • 0

Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…

Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k

That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…

Votes

Answer: get BM error

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

Comment: Different Shrunk Log2FC according with reference

Reproducibility issue with scran together with lapply and BiocParallel

C: SGSeq: moving toward diffex from SGSeq analysis

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