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Views
Votes
1
vote
7
replies
182
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
2 days ago • updated 1 day ago
pl23
• 0
1
vote
2
replies
206
views
MethylKit read issue
methylKit
updated 21 days ago by
James W. MacDonald
65k • written 27 days ago by
CHEN
• 0
1
vote
3
replies
821
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 3 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
379
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
10 days ago • updated 1 day ago
ussarizona
▴ 10
1
vote
2
replies
223
views
How to retrieve detailed regression results from deseq2
DESeq2
16 days ago • updated 8 days ago
Weiqian
▴ 10
1
vote
0
replies
212
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
8 days ago
BioinfGuru
▴ 30
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 26 days ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
1
vote
13
replies
305
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
6 days ago • updated 2 days ago
fernanda.backsouza
▴ 10
1
vote
3
replies
122
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 1 day ago by
Michael Love
41k • written 1 day ago by
JalapenoCornbread
• 0
1
vote
3
replies
327
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 12 days ago by
Gordon Smyth
50k • written 17 days ago by
Simran
• 0
1
vote
2
replies
937
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 4 days ago by
Tim Peters
▴ 170 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
191
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
9 days ago • updated 8 days ago
Le
• 0
1
vote
1
reply
102
views
Citation for edgeR user guide
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
k___
▴ 30
1
vote
7
replies
1.7k
views
Error using champ.import
ChAMP
EPICv2
updated 10 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
1
vote
6
replies
463
views
GSVA on separate healthy and disease datasets
GSVA
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
Lucy
▴ 60
1
vote
1
reply
70
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 4 days ago by
James W. MacDonald
65k • written 4 days ago by
fernanda.backsouza
▴ 10
1
vote
3
replies
137
views
Different Shrunk Log2FC according with reference
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
416
views
GSVA error
GSVA
13 days ago • updated 12 days ago
Alex
• 0
1
vote
4
replies
153
views
minfi::read.metharray.exp
minfiData
minfi
updated 3 days ago by
Basti
▴ 780 • written 5 days ago by
clacarion
• 0
1
vote
4
replies
166
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 5 days ago by
James W. MacDonald
65k • written 9 days ago by
Mirella Aurora
• 0
1
vote
4
replies
417
views
Using a change in a continuous explanatory variable to test changes in gene expression with limma
limma
updated 22 days ago by
Gordon Smyth
50k • written 24 days ago by
jari.karppinen
• 0
1
vote
10
replies
411
views
Obtaining pheno data from CEL files
GEO
affy
25 days ago • updated 18 days ago
Kurtis
• 0
1
vote
2
replies
129
views
Error in champ.load(): The following specified files do not exist
ChAMP
9 days ago
Sherin
• 0
1
vote
2
replies
175
views
Design Matrix within group comparison more than two groups
DESeq2
15 days ago • updated 14 days ago
hemantcnaik
• 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 22 days ago by
Michael
▴ 10 • written 24 months ago by
axe880
• 0
1
vote
1
reply
58
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 20 hours ago by
Leo Lahti
▴ 40 • written 1 day ago by
Dario Strbenac
★ 1.5k
1
vote
6
replies
407
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 23 days ago by
Michael Love
41k • written 24 days ago by
RL
• 0
1
vote
4
replies
205
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
3 days ago • updated 1 day ago
winwater0928
• 0
1
vote
3
replies
231
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 21 days ago by
James W. MacDonald
65k • written 22 days ago by
Shaimaa Gamal
• 0
1
vote
1
reply
156
views
DESeq2 - Missing values in count matrix
DESeq2
updated 23 days ago by
James W. MacDonald
65k • written 23 days ago by
Hong Thu
• 0
1
vote
1
reply
166
views
Differentially expressed genes in monocle pseudotime
monocle
updated 11 days ago by
Gordon Smyth
50k • written 13 days ago by
kthapa
• 0
0
votes
6
replies
3.1k
views
limma, analysis on subset of data gives completely different results
limma
limma
updated 25 days ago by
Gordon Smyth
50k • written 9.8 years ago by
Arvid Sondén
▴ 40
0
votes
0
replies
116
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
17 days ago
Eryn
• 0
0
votes
0
replies
73
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
15 days ago
shepherl
3.8k
0
votes
1
reply
121
views
Bioinformatics student
Des
DESeq2
updated 15 days ago by
hemantcnaik
• 0 • written 15 days ago by
Sahar
• 0
0
votes
2
replies
166
views
Gene Ontology doubt
microbiomeExplorer
26 days ago • updated 22 days ago
Bhawna
• 0
0
votes
2
replies
334
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 24 days ago
Gordon
• 0
0
votes
3
replies
232
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 9 days ago by
W. Evan Johnson
▴ 850 • written 15 days ago by
schlumbohm
• 0
0
votes
1
reply
145
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 25 days ago by
James W. MacDonald
65k • written 26 days ago by
ja569116
• 0
0
votes
0
replies
79
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
17 days ago
Dennis
• 0
0
votes
4
replies
396
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
26 days ago • updated 25 days ago
Lucy
▴ 60
0
votes
2
replies
157
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
4 days ago • updated 2 days ago
shuwangxinze1996
• 0
0
votes
7
replies
391
views
DESeq filtering specific to contrasts
DESeq2
updated 8 days ago by
Michael Love
41k • written 10 weeks ago by
Emma
• 0
0
votes
1
reply
129
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 25 days ago by
James W. MacDonald
65k • written 25 days ago by
Reeya
• 0
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
27 days ago • updated 8 days ago
isaac.vock
• 0
0
votes
0
replies
85
views
News:
Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry
conference
19 days ago
Wolfgang Huber
★ 13k
0
votes
2
replies
148
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
joshua.mannheimer
• 0
0
votes
1
reply
92
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 9 days ago by
Alejandro Reyes
★ 1.9k • written 9 days ago by
Alessia
• 0
0
votes
3
replies
316
views
Statistical test
NewWave
written 4 months ago by
mario
• 0
0
votes
1
reply
167
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler
ggpubr
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
BCS12
• 0
194 results • Page
2 of 4
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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