0
votes
9
replies
1.5k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin DESeq2
updated 7 months ago by ▴ 10 • written 22 months ago by ▴ 10
4
votes
9
replies
448
views
Memory errors using read.bismark?
dmrseq bsseq
29 days ago • updated 3 days ago Juan Higareda • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 22 days ago by 50k • written 7 months ago by ▴ 10
1
vote
9
replies
891
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
4
votes
9
replies
4.4k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.9 years ago by • 0
6
votes
9
replies
802
views
biomaRt has encountered an unknown server error.
biomaRt host useEnsembl
updated 3 months ago by • 0 • written 3 months ago by • 0
5
votes
9
replies
941
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
4 weeks ago • updated 22 days ago Chris • 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
0
votes
9
replies
569
views
limma fo continous variables
limma DEGseq
updated 10 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi bumphunter
updated 11 months ago by • 0 • written 6.2 years ago by • 0
2
votes
9
replies
406
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 15 days ago by 65k • written 15 days ago by • 0
0
votes
9
replies
857
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
8 months ago mjd275 • 0
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib rhdf5
3.2 years ago • updated 8 months ago Thomas Sandmann ▴ 90
0
votes
8
replies
719
views
Deseq2 Results are different using batch design
DESeq2
9 months ago hemantcnaik • 0
3
votes
8
replies
920
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
0
votes
8
replies
8.6k
views
Bioconductor version cannot be validated
BiocManager Bioconductor
updated 5 months ago by 690 • written 2.8 years ago by ▴ 10
0
votes
8
replies
424
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
9 weeks ago michelafrancesconi8 • 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge beta DESeq2
11 months ago Ndimensional ▴ 20
3
votes
8
replies
530
views
Downloading package mixOmics
mixOmics
11 weeks ago noortje_bloem94 • 0
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
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by ▴ 60
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago Luis • 0
2
votes
8
replies
1.3k
views
Reading GFF file and pre-processing, run iinfer_syntenet(), input and output
syntenet
updated 4 months ago by • 0 • written 16 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
3
votes
8
replies
528
views
Constrast for Time Course Experiments using Limma
limma
9 weeks ago dl17032000 • 0
8
votes
8
replies
9.8k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2 DESeq2
updated 7 months ago by • 0 • written 4.8 years ago by ▴ 40
0
votes
8
replies
361
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 15 days ago by ★ 1.4k • written 17 days ago by • 0
0
votes
8
replies
1.1k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray TileDBArray
8 months ago sandmann.t ▴ 70
2
votes
8
replies
550
views
Microarray Limma Model fitting and DEG
limma DGEanalysis
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.4 years ago by ▴ 10
1
vote
8
replies
1.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 11 months ago by • 0
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by • 0 • written 6.8 years ago by ▴ 30
0
votes
8
replies
828
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 14 months ago by • 0
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData MicroarrayData limma
updated 5 months ago by • 0 • written 11 months ago by ▴ 10
1
vote
8
replies
554
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
8
replies
1.4k
views
Question about filterByExpr function edgeR
edgeR
8 months ago lucap • 0
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago Habil Zare ▴ 200
0
votes
8
replies
1.7k
views
flowset/ncdfFlowset replace keywords doesn't work right
ncdfFlow flowCore
updated 7 months ago by • 0 • written 3.6 years ago by ▴ 30
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 17 days ago by • 0 • written 7.7 years ago by ▴ 30
1
vote
8
replies
1.3k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 5 weeks ago by ★ 13k • written 10 months ago by ▴ 10
0
votes
8
replies
717
views
GOslim missing GO term
GO.db GOslim
5 months ago amanda • 0
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 11 months ago by 50k • written 17 months ago by ▴ 20
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 21 months ago by ▴ 10
0
votes
8
replies
652
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago Marianna ▴ 20
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
1
vote
7
replies
872
views
Permutation test in DESeq2?
DESeq2
updated 7 months ago by 42k • written 7 months ago by • 0
3
votes
7
replies
892
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
8 months ago casco ▴ 10
8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by ▴ 30
1,742 results • Page 3 of 35
Recent ...
Replies
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
France, 11 minutes ago
United States, 15 minutes ago
United States, 17 minutes ago
United States, 57 minutes ago
EMBL Heidelberg, 1 hour ago
Traffic: 684 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