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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
159
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
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
233
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 27 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 28 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 28 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
157
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
328
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 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
226
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
5 weeks ago • updated 4 weeks ago
w.cookson
• 0
0
votes
2
replies
166
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago • updated 29 days ago
michelafrancesconi8
• 0
0
votes
1
reply
140
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Reeya
• 0
0
votes
4
replies
253
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
4
replies
414
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago
Lucy
▴ 60
0
votes
1
reply
107
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Leyre
• 0
0
votes
2
replies
179
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
4 weeks ago
Seongsu
• 0
0
votes
2
replies
174
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 28 days ago
Bhawna
• 0
0
votes
1
reply
168
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
156
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
ja569116
• 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
252
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
7
replies
387
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
4 weeks ago
needNGS
• 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
3
votes
5
replies
371
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Fabian
• 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
0
votes
0
replies
109
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
4 weeks ago
feather-W
• 0
0
votes
0
replies
108
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
4 weeks ago
Ankit
▴ 20
0
votes
6
replies
348
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Faisal
• 0
1
vote
5
replies
331
views
fgsea fork
fgsea
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
yimjohns
• 0
0
votes
1
reply
158
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Mikushi
• 0
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
518
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
0
votes
1
reply
134
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Karen
• 0
2
votes
3
replies
345
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Laura
▴ 10
1
vote
2
replies
227
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
5 weeks ago
Mj.A.
• 0
0
votes
1
reply
257
views
News:
Bioconductor 3.19 Release Schedule
Release
release
Software
8 weeks ago • updated 5 weeks ago
shepherl
3.9k
0
votes
2
replies
205
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
SG
• 0
2
votes
3
replies
252
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 5 weeks ago by
Wei Shi
★ 3.6k • written 5 weeks ago by
thomas.heigl.ibk
• 0
2
votes
2
replies
217
views
From a DNAStringSet to a data.frame
Biostrings
5 weeks ago
ramiro.barrantes
▴ 10
0
votes
1
reply
168
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Léa
• 0
45,611 results • Page
4 of 913
Recent ...
Replies
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.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
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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