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78
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Input Question for deseq.r
RSeqAn
updated 6 days ago by ★ 4.0k • written 7 days ago by • 0
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4
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191
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 4 days ago lonn • 0
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Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
7 days ago • updated 1 day ago hortense96 • 0
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334
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Memory errors using read.bismark?
dmrseq bsseq
updated 5 days ago by ▴ 740 • written 13 days ago by • 0
3
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165
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Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
12 days ago • updated 6 days ago jacques.imbert • 0
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215
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How to retrieve detailed regression results from deseq2
DESeq2
13 days ago • updated 5 days ago Weiqian ▴ 10
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228
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DEG with low counts
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updated 5 days ago by 41k • written 9 days ago by • 0
3
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permutation test in edgeR
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A ComBat-seq issue: the covariates are confounded
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Light difference when using coef vs omit a group when compare 3 groups.
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13 days ago • updated 6 days ago Chris • 0
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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The difference when using Limma compare between 3 conditions vs 2 conditions
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26 days ago • updated 4 days ago Chris • 0
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Estimating Cell Counts for EPIC V2 array data
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DESeq filtering specific to contrasts
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updated 5 days ago by 41k • written 9 weeks ago by • 0
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Batch correction and repeated measures
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problem installing ENmix package
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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updated 9 hours ago by ★ 1.2k • written 13 months ago by ▴ 10
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Which input file is used for DGEList in EgdeR?
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updated 5 days ago by • 0 • written 14 months ago by ▴ 10
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896
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Problem for loading Bioconductor package in R
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written 4.2 years ago by • 0
6
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16
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2.2k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
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updated 1 day ago by 41k • written 4.6 years ago by ▴ 10
2
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5
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694
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DESeq2 setting significant p-value
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Job: Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
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Limma design with continuous and categorical covariates
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Multi factor design edgeR/Deseq2
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updated 6 days ago by • 0 • written 8.8 years ago by ▴ 30
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 5 days ago by • 0 • written 9.1 years ago by ▴ 150
76 results • Page 2 of 2
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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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