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10
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451
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Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 25 days ago
Kurtis
• 0
0
votes
1
reply
162
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 28 days ago by
Gordon Smyth
50k • written 28 days ago by
avery
• 0
1
vote
3
replies
246
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
227
views
MethylKit read issue
methylKit
updated 28 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 28 days ago by
Michael
▴ 10 • written 2.0 years ago by
axe880
• 0
0
votes
4
replies
306
views
Help with design.matrix
limma
28 days ago • updated 27 days ago
andrea.rodriguez-martinez13
• 0
0
votes
0
replies
143
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
28 days ago
andromeda
• 0
0
votes
2
replies
165
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
joshua.mannheimer
• 0
2
votes
2
replies
188
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 28 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
128
views
Granges regionCounts not returning the expected number of entries
methylKit
29 days ago • updated 28 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
100
views
flowDensity on a flowset
flowDensity
29 days ago
fredrikwallberg
• 0
1
vote
1
reply
164
views
DESeq2 - Missing values in count matrix
DESeq2
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
Hong Thu
• 0
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 29 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
1
vote
2
replies
276
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
4 weeks ago • updated 15 hours ago
Kim
• 0
0
votes
0
replies
90
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
4 weeks ago
Macsue
• 0
1
vote
4
replies
437
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
jari.karppinen
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 4 weeks ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
0
votes
2
replies
760
views
error in install immunedeconv
Install
updated 4 weeks ago by
Arash
• 0 • written 13 months ago by
fenglingao
• 0
1
vote
6
replies
430
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
RL
• 0
0
votes
2
replies
186
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
4 weeks ago
Gimena
• 0
0
votes
2
replies
166
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
4 weeks ago
Marianna
▴ 20
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 4 weeks ago by
Tim Peters
▴ 180 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
6
replies
332
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 23 days ago by
Tim Peters
▴ 180 • written 4 weeks ago by
s.malik
• 0
1
vote
1
reply
152
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago
Layal
• 0
0
votes
2
replies
228
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
171
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago
michelafrancesconi8
• 0
0
votes
1
reply
141
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
257
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
418
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
109
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
181
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
4 weeks ago
Seongsu
• 0
0
votes
2
replies
176
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 29 days ago
Bhawna
• 0
0
votes
1
reply
170
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 4 weeks ago by
Michael Love
41k • written 5 weeks ago by
saadmurtazakhan
▴ 10
0
votes
1
reply
159
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
294
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 28 days ago
fer_talavera
• 0
0
votes
2
replies
254
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 14 days ago
isaac.vock
• 0
0
votes
7
replies
391
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
5 weeks ago • updated 3 days ago
Chris
• 0
3
votes
5
replies
377
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
240
views
Minfi - estimatecellscount
min
minfi
updated 4 days ago by
James W. MacDonald
65k • written 5 weeks ago by
clacarion
• 0
0
votes
0
replies
110
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
5 weeks ago
feather-W
• 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
5 weeks ago
Ankit
▴ 20
0
votes
6
replies
352
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Faisal
• 0
1
vote
5
replies
338
views
fgsea fork
fgsea
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
yimjohns
• 0
0
votes
1
reply
160
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
96
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
2
votes
8
replies
523
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
136
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
347
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
229
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
1,743 results • Page
4 of 35
Recent ...
Replies
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…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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