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Votes
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.0 years ago by
Marianna
▴ 20
3
votes
7
replies
5.4k
views
error with champ.load
champ
written 6.5 years ago by
o.giannakopoulou
▴ 10
2
votes
6
replies
1.3k
views
Unable to load data from duffel.rail
recount
recountWorkflow
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
Max Bone
• 0
0
votes
11
replies
2.0k
views
globaltest question
Pathways
probe
affy
Pathways
probe
affy
written 17.6 years ago by
mike Ad.
▴ 30
0
votes
17
replies
3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2
differential expression
error
updated 10 months ago by
snow34
• 0 • written 6.6 years ago by
ap3637
• 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
2
votes
2
replies
383
views
"Details" section for specific software packages
Website
updated 6 months ago by
Mike Smith
★ 6.5k • written 6 months ago by
Justin
• 0
1
vote
3
replies
1.8k
views
Making MDS plot
plotMDS
limma
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
liujy4
• 0
2
votes
3
replies
2.1k
views
Keep getting this error "Warning: unable to access index for repository"?
CATALYST
updated 11 months ago by
Hervé Pagès
16k • written 11 months ago by
Hyoann
▴ 20
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
1
vote
8
replies
2.7k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.1 years ago by
serpalma.v
▴ 60
0
votes
2
replies
680
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
dml
• 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 9 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
0
votes
4
replies
863
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 8 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 24 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
1
vote
2
replies
255
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
1
vote
3
replies
451
views
DESeq2: the model matrix is not full rank issue
DESeq2
updated 4 months ago by
malliardtee
• 0 • written 4 months ago by
Guangsheng
• 0
2
votes
3
replies
2.2k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 6 weeks ago by
ATpoint
★ 4.0k • written 2.1 years ago by
liqidong52
▴ 20
0
votes
2
replies
543
views
Heat Map
ColData
pheatmap
DESeq2
written 10 months ago by
dania.khalid
• 0
0
votes
2
replies
804
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Juan Pablo
• 0
2
votes
3
replies
298
views
seqlevelsStyle() not working
ensembldb
genomei
GenomeInfoDb
11 weeks ago
Kai Hu
▴ 70
1
vote
4
replies
171
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
5
votes
5
replies
434
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
12 weeks ago • updated 11 weeks ago
baptiste
▴ 20
1
vote
3
replies
1.4k
views
Error in the UcscTrack() in package "Gviz"
DMR
Methylation
R
Gviz
updated 5 months ago by
Robert Ivanek
▴ 730 • written 3.0 years ago by
ltzhou
• 0
2
votes
6
replies
763
views
Biostrings error at retrieving protein sequences
SequenceMatching
Biostrings
DifferentialExpression
Proteome
updated 6 months ago by
Hervé Pagès
16k • written 6 months ago by
nromerov
• 0
0
votes
2
replies
566
views
DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
Anonymous Genetics Gnome
• 0
1
vote
5
replies
552
views
ChIPpeakAnno annotatePeakInBatch output
ChIPpeakAnno
6 months ago
ilaria.maurizio
• 0
1
vote
3
replies
384
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 12 weeks ago by
pl23
• 0
1
vote
2
replies
651
views
unable to retrieve certain packages from bioconductor 3.15
Bioconductor
biocondu
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Ashton
▴ 10
2
votes
5
replies
1.3k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2
BatchEffect
limma
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
Sara
• 0
3
votes
3
replies
341
views
plotUMAP Gene Set Faceted
scater
updated 12 weeks ago by
alan.ocallaghan
▴ 160 • written 12 weeks ago by
Dario Strbenac
★ 1.5k
7
votes
2
replies
1.2k
views
Format roxgen comment (alternative to formatR)
BiocCheck
written 2.6 years ago by
ZheFrench
▴ 50
1
vote
5
replies
666
views
edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
alex.hart
• 0
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 6 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
0
votes
4
replies
361
views
Extract LRT results for each comparison
LRT
DESeq2
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Yijing
• 0
28
votes
21
replies
48k
views
deseq2 filter the low counts
deseq2
lowcount
updated 3 months ago by
Xiao
• 0 • written 9.2 years ago by
aristotele_m
▴ 40
0
votes
2
replies
260
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
z_bahari
• 0
0
votes
2
replies
310
views
Complex DESeq2 Experimental Design
DESEq2
DESeq2
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
Elizabeth
• 0
8
votes
12
replies
2.5k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 11 months ago by
Michael Love
41k • written 12 months ago by
Michael Steinbaugh
▴ 90
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
9 months ago
Luca
• 0
0
votes
2
replies
168
views
bioconductor emailing list
Bioconductor
updated 4 weeks ago by
shepherl
3.8k • written 4 weeks ago by
1427972815
• 0
0
votes
2
replies
790
views
Recount3 data download problem
recount
recount3
updated 11 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
franceschini.gianmarco
• 0
0
votes
4
replies
1.9k
views
how to save subsetted GDS file
gwastools
written 6.0 years ago by
Adrienne Stilp
▴ 30
7
votes
6
replies
4.1k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 6 months ago by
Marcel Ramos
690 • written 20 months ago by
Recep
▴ 20
4
votes
7
replies
845
views
weird volcano plot
DESeq2
updated 7 weeks ago by
Shuning
• 0 • written 5 months ago by
shouzheng
▴ 10
6
votes
5
replies
6.1k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 7 months ago by
Gordon Smyth
50k • written 2.5 years ago by
David Lyon
▴ 340
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge
beta
DESeq2
10 months ago
Ndimensional
▴ 20
0
votes
5
replies
698
views
Wondering how to look at the reads of a gene in samples to check if it was knocked out?
knockout
DESeq2
written 10 months ago by
Lillian
• 0
0
votes
2
replies
468
views
EdgeR FTest
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
nawaz.u.toyama
• 0
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 5 days ago
shepherl
3.8k
1,732 results • Page
2 of 35
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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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