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0
votes
4
replies
302
views
Help with design.matrix
limma
27 days ago • updated 26 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
142
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
27 days ago
andromeda
• 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
185
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 27 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
127
views
Granges regionCounts not returning the expected number of entries
methylKit
28 days ago • updated 27 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
98
views
flowDensity on a flowset
flowDensity
28 days ago
fredrikwallberg
• 0
1
vote
1
reply
160
views
DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
Hong Thu
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 28 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
0
votes
1
reply
235
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
updated 28 days ago by
Tim Peters
▴ 170 • written 29 days ago by
Kim
• 0
0
votes
0
replies
88
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
28 days ago
Macsue
• 0
1
vote
4
replies
428
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 29 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
754
views
error in install immunedeconv
Install
updated 29 days ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
419
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 29 days ago by
Michael Love
41k • written 29 days ago by
RL
• 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago
Gimena
• 0
0
votes
2
replies
159
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
29 days ago
Marianna
▴ 20
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 29 days ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
330
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 22 days ago by
Tim Peters
▴ 170 • written 4 weeks ago by
s.malik
• 0
1
vote
1
reply
150
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago
Layal
• 0
0
votes
2
replies
167
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago • updated 29 days ago
michelafrancesconi8
• 0
0
votes
2
replies
174
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 28 days ago
Bhawna
• 0
0
votes
2
replies
288
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 27 days ago
fer_talavera
• 0
0
votes
2
replies
253
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
0
votes
4
replies
237
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
5
votes
25
replies
881
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
6
votes
5
replies
419
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
1
vote
4
replies
456
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
0
votes
7
replies
406
views
DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
2
votes
5
replies
1.0k
views
STRINGdb R package reference class instantiation with v12.0
STRINGdb
updated 27 days ago by
damian.szk
▴ 80 • written 5 months ago by
Abhishek
• 0
0
votes
2
replies
781
views
Job:
Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia)
bioconductor
artificialintelligence
JobPosting
machinelearning
written 8 months ago by
Gordon Smyth
50k
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 16 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
1
reply
336
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 22 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 15 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
0
votes
4
replies
5.2k
views
SingleR Label.Ont
SingleR
updated 17 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 15 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 15 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
1
vote
3
replies
850
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 8 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 19 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
507
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 23 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
0
votes
2
replies
907
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 15 days ago by
wichaidi
• 0 • written 17 months ago by
irvin.ng
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 9 hours ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
1
reply
551
views
CopywriteR output
CopywriteR
updated 27 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
3
votes
1
reply
752
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
0
votes
2
replies
915
views
Problem for loading Bioconductor package in R
Bioconductor
written 4.2 years ago by
araaaju
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
5
replies
736
views
DESeq2 setting significant p-value
DESeq2
updated 13 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
206 results • Page
4 of 5
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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