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Views
Votes
2
votes
2
replies
237
views
fgsea significant result
fgsea
16 days ago • updated 15 days ago
Chris
▴ 10
1
vote
1
reply
196
views
Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
Zainab
▴ 10
2
votes
3
replies
264
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Reza
• 0
0
votes
6
replies
307
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 17 days ago by
swbarnes2
★ 1.4k • written 18 days ago by
arfranco
▴ 130
1
vote
2
replies
409
views
limma Intercept vs No-intercept models completely changing DMR results?
limma
DMRcate
MethylationArray
EPICV2
updated 17 days ago by
Gordon Smyth
50k • written 17 days ago by
Kim
• 0
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
19 days ago • updated 17 days ago
Chris
▴ 10
1
vote
2
replies
390
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 17 days ago
Kim
• 0
0
votes
0
replies
125
views
dba.plotProfile() plotting and interpretation
DiffBind
18 days ago
Henry
▴ 10
0
votes
2
replies
172
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
21 days ago • updated 18 days ago
Aurora
• 0
0
votes
0
replies
145
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
26 days ago • updated 18 days ago
glaciya2018
• 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago
kcarey
• 0
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
z_bahari
• 0
0
votes
1
reply
166
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
c53aba27
• 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
19 days ago
tholmes
• 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 19 days ago by
James W. MacDonald
66k • written 2.4 years ago by
yanchangjian2019
• 0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
19 days ago
yvonneh
• 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 days ago
Ian D.
▴ 70
0
votes
1
reply
145
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by
4r-rtg
• 0
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 19 days ago by
ATpoint
★ 4.1k • written 19 days ago by
james.zhang20
• 0
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 28 days ago by
taur.vil
• 0
1
vote
2
replies
297
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
20 days ago • updated 19 days ago
Yveto
• 0
0
votes
3
replies
305
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
HAK
• 0
4
votes
0
replies
147
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
19 days ago
shepherl
3.9k
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago
Chris
▴ 10
1
vote
4
replies
533
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 19 days ago
JKim
• 0
3
votes
4
replies
270
views
Help with error using camera() in limma
CAMERA
limma
21 days ago • updated 20 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 20 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 20 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
267
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 20 days ago by
James W. MacDonald
66k • written 21 days ago by
SSSJec
• 0
0
votes
3
replies
283
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 21 days ago by
James W. MacDonald
66k • written 22 days ago by
SSSJec
• 0
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 21 days ago
Chris
▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 21 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
192
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 21 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
marcusn
• 0
0
votes
1
reply
141
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by
Michael Love
42k • written 21 days ago by
Agung
• 0
0
votes
0
replies
96
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
21 days ago
Maria Doyle
▴ 70
0
votes
1
reply
127
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 21 days ago by
shepherl
3.9k • written 21 days ago by
bounlu
• 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Dev
• 0
2
votes
2
replies
240
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago
Chris
▴ 10
0
votes
0
replies
98
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
22 days ago
Chris
▴ 10
0
votes
4
replies
267
views
Minfi - estimatecellscount
min
minfi
updated 22 days ago by
James W. MacDonald
66k • written 7 weeks ago by
clacarion
• 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 22 days ago by
ATpoint
★ 4.1k • written 22 days ago by
bioinf
▴ 10
0
votes
0
replies
101
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
27 days ago • updated 22 days ago
Sara
• 0
1
vote
1
reply
155
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 24 days ago by
Leo Lahti
▴ 40 • written 25 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
26 days ago • updated 25 days ago
pl23
• 0
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2
PCAtools
updated 25 days ago by
Michael Love
42k • written 26 days ago by
Aaliya
• 0
1
vote
2
replies
757
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago
Patadù
▴ 10
1
vote
3
replies
257
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 25 days ago by
Michael Love
42k • written 25 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
175
views
ATACseq merge peaks
DiffBind
updated 25 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Shloka
• 0
1,000 results • Page
3 of 20
Recent ...
Replies
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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