6
votes
7
replies
764
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 15 days ago by • 0 • written 15 months ago by ▴ 10
6
votes
7
replies
566
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges grangeslist overlapsAny
updated 20 days ago by • 0 • written 8.0 years ago by ▴ 180
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache AnnotationHub ExperimentHub
6 months ago • updated 12 days ago shepherl 3.9k
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by ▴ 180 • written 17 months ago by ▴ 30
6
votes
5
replies
6.2k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 7 months ago by 50k • written 2.5 years ago by ▴ 340
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
6
votes
5
replies
1.2k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 8 months ago by ▴ 740 • written 9 months ago by ▴ 20
5
votes
1
reply
437
views
News: Bioconductor 3.18 is Released!
Packages Bioconductor Release Software
written 6 months ago by 3.9k
5
votes
5
replies
796
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 11 days ago by • 0 • written 7.7 years ago by ▴ 30
5
votes
9
replies
918
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
23 days ago • updated 16 days ago Chris • 0
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 3 months ago by • 0 • written 14 months ago by ▴ 70
5
votes
5
replies
1.9k
views
Archive location for Bioconductor packages
archive
updated 8 months ago by 3.9k • written 20 months ago by ▴ 20
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
5
votes
3
replies
2.0k
views
Cannot download GEOmetadb sqlite file
GEOmetadb
updated 3 months ago by • 0 • written 6.5 years ago by ▴ 10
5
votes
6
replies
424
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 days ago by ★ 4.1k • written 25 days ago by ▴ 30
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by • 0
5
votes
6
replies
652
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 7 months ago by 16k • written 7 months ago by ★ 1.5k
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
5
votes
3
replies
704
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 6 months ago by 50k • written 6 months ago by ▴ 180
5
votes
2
replies
557
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 5 months ago by • 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
5
votes
2
replies
867
views
can't install DESeq2 ("unable to access index for repository")
biocmanager DESeq2
8 months ago Alessia ▴ 40
5
votes
4
replies
392
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
5
votes
7
replies
454
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 5 weeks ago by 50k • written 7 weeks ago by • 0
5
votes
2
replies
682
views
outdated GEOmetadb.sqlite
GEOmetadb
14 months ago • updated 3 months ago Robert Castelo ★ 3.3k
5
votes
4
replies
9.7k
views
Getting rs ids using chr coordinates | Biomart
SNP rs id Biomart Chromosome coordinates
updated 9 months ago by 65k • written 3.7 years ago by • 0
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor Install DESeq2
updated 4 months ago by • 0 • written 2.3 years ago by • 0
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.5 years ago by ▴ 10
5
votes
6
replies
549
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 2 days ago by 65k • written 2.3 years ago by • 0
5
votes
6
replies
1.9k
views
Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
5 months ago kjngo ▴ 40
5
votes
2
replies
753
views
ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
7 months ago Federico ▴ 10
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
5
votes
2
replies
689
views
PhD student
TMM limma
10 months ago Nisha • 0
5
votes
3
replies
712
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
5
votes
25
replies
913
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 29 days ago by 50k • written 5 weeks ago by ▴ 10
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 16 days ago by 50k • written 7 months ago by ▴ 10
5
votes
5
replies
441
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
3 months ago • updated 12 weeks ago baptiste ▴ 20
5
votes
6
replies
849
views
ASpli checks fail on Linux due to missing dependency to statmod
ASpli
updated 9 months ago by 50k • written 9 months ago by ▴ 10
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 7.9 years ago by • 0
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 5 months ago by 50k • written 3.5 years ago by ★ 4.1k
4
votes
2
replies
629
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
1,000 results • Page 2 of 20
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
United States, 29 minutes ago
India, 37 minutes ago
Ireland, 53 minutes ago
France, 1 hour ago
United States, 1 hour ago
Traffic: 595 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6