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1
vote
5
replies
852
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
8 months ago
duez.tolga
• 0
0
votes
3
replies
372
views
LOG2FC DESEQ2
DESeq2
updated 3 months ago by
Michael Love
41k • written 3 months ago by
ilaria.montali
• 0
0
votes
2
replies
360
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 8 weeks ago by
ATpoint
★ 4.1k • written 9 weeks ago by
Suvi
• 0
4
votes
14
replies
3.5k
views
Data input for aracne2regulon function in viper package
viper
updated 3 months ago by
YNPAN910
• 0 • written 4.7 years ago by
maya.kappil
▴ 30
1
vote
11
replies
1.0k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 6 months ago by
Michael Love
41k • written 6 months ago by
cm15245
• 0
2
votes
1
reply
264
views
Need Help w/ Subset on GRangesList
GenomicRange
GenomicRanges
3 months ago • updated 12 weeks ago
mat149
▴ 70
1
vote
3
replies
345
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 19 days ago by
Gordon Smyth
50k • written 24 days ago by
Simran
• 0
1
vote
2
replies
267
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
4
votes
4
replies
431
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
5
votes
4
replies
9.7k
views
Getting rs ids using chr coordinates | Biomart
SNP
rs id
Biomart
Chromosome
coordinates
updated 9 months ago by
James W. MacDonald
65k • written 3.7 years ago by
Mahan
• 0
10
votes
8
replies
3.9k
views
conumee error: query intensities not given for all probes.
conumee
updated 4 months ago by
Mingkee
• 0 • written 6.8 years ago by
yura.grabovska
▴ 30
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 20 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
1
vote
3
replies
402
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
0
votes
9
replies
837
views
How long does it usually take to complete dream() from start to finish?
variancePartition
mixedmodel
dream
8 months ago
hayleyw
• 0
1
vote
4
replies
734
views
MDS plot edgeR
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
jbono
▴ 10
1
vote
3
replies
1.7k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 4.1 years ago by
hasse.bossenbroek
• 0
1
vote
8
replies
1.5k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression
DESeq2
written 10 months ago by
sean.mccutcheon
• 0
0
votes
3
replies
777
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 8 months ago by
Hervé Pagès
16k • written 9 months ago by
anavmar1
• 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by
James W. MacDonald
65k • written 11 months ago by
kyliecode
• 0
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
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 4 months ago by
picasa1983
• 0 • written 2.3 years ago by
Victor
• 0
3
votes
3
replies
976
views
Rlog performed on tpm or raw transcript abundances?
DESeq2
rlog
written 17 months ago by
Bioinformatics-414
• 0
0
votes
2
replies
693
views
Cannot download data from IDIES links
recount
recountWorkflow
recount3
updated 12 months ago by
Leonardo Collado Torres
★ 1.0k • written 16 months ago by
dml
• 0
0
votes
4
replies
372
views
Extract LRT results for each comparison
LRT
DESeq2
updated 7 months ago by
ATpoint
★ 4.1k • written 7 months ago by
Yijing
• 0
8
votes
9
replies
1.1k
views
All three of the sites where genomeinfodbdata R packages are stored appear to be down.
GenomeInfoDbData
8 months ago
15753563659
▴ 50
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.5 years ago by
knaxerova
▴ 10
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
13 days ago • updated 2 days ago
Chris
• 0
1
vote
2
replies
415
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Jurgen
• 0
0
votes
4
replies
2.6k
views
Error using Bsmooth.tstat due to NAs
Coverage
bsseq
updated 6 months ago by
Adam
• 0 • written 9.7 years ago by
Guest User
★ 13k
0
votes
4
replies
880
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
8
replies
909
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 5 months ago by
pcantalupo
▴ 10
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi
bumphunter
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
src3
• 0
0
votes
4
replies
3.1k
views
Problems with FLOWAI
flowAI
written 3.0 years ago by
msoares
• 0
6
votes
5
replies
6.2k
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
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
1
vote
3
replies
595
views
Read Count Normalisation and validation of analysis
DifferentialExpression
DESeq2
written 4 months ago by
Dinesh
• 0
2
votes
6
replies
341
views
Factor vs Character in design
DESeq2
8 weeks ago
James Aiden
• 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport
tximportData
DESeq2
10 months ago
Ndimensional
▴ 20
3
votes
6
replies
22k
views
Deseq: What does "BaseMean" mean?
deseq2
updated 3 months ago by
kledo577
• 0 • written 5.6 years ago by
183227851
• 0
0
votes
5
replies
921
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
6 months ago
dorota.komar
• 0
7
votes
5
replies
6.9k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 6 months ago by
Ke
• 0 • written 2.0 years ago by
kieran.short
▴ 40
1
vote
2
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 11 months ago by
brukti
• 0 • written 8.6 years ago by
akridgerunner
▴ 30
0
votes
2
replies
294
views
Error in featureCounts matrix
GenomeWideAssociation
countsimQC
RNASeq
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
ryann
• 0
0
votes
2
replies
876
views
News:
List of Deprecated Packages for Bioc3.17
Bioconductor
Deprecation
Devel
devel
12 months ago • updated 11 months ago
shepherl
3.9k
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
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 6 weeks ago by
Eva
• 0 • written 7.6 years ago by
ctl
• 0
5
votes
2
replies
554
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
3
votes
4
replies
1.8k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
12 months ago
Mark
• 0
1
vote
3
replies
324
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
9 weeks ago • updated 8 weeks ago
I-Hsuan Lin
▴ 10
2
votes
3
replies
797
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 11 months ago by
jandrade
• 0
1,743 results • Page
3 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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