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4
votes
9
replies
1.3k
views
DittoDimPlot errror: Cannot find 'NA' in this Seurat object
dittoSeq
updated 8 months ago by
dbunis
▴ 10 • written 8 months ago by
nina.hahn
▴ 10
0
votes
9
replies
1.4k
views
ranking the DeSeq2 results using t-values?
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Theo
▴ 10
2
votes
9
replies
1.8k
views
How to load fasta file with openPrimeR?
openPrimeR
written 3.2 years ago by
marongiu.luigi
• 0
0
votes
9
replies
1.5k
views
Questions about the false positives indicated by DESeq2 and QQ plot
pre-filterin
DESeq2
updated 7 months ago by
yujin
▴ 10 • written 22 months ago by
Weiqian
▴ 10
4
votes
9
replies
436
views
Memory errors using read.bismark?
dmrseq
bsseq
27 days ago • updated 23 hours ago
Juan Higareda
• 0
1
vote
9
replies
890
views
DESeq2 not replicable results
RNASeqData
DESeq2
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Matteo
• 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
0
votes
9
replies
855
views
DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
8 months ago
mjd275
• 0
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
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
2
votes
9
replies
396
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 12 days ago by
James W. MacDonald
65k • written 13 days ago by
Alexandre
• 0
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib
rhdf5
3.2 years ago • updated 8 months ago
Thomas Sandmann
▴ 90
2
votes
8
replies
544
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
5
votes
8
replies
1.5k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 4 months ago by
Shaimaa Gamal
• 0 • written 11 months ago by
pg45863
▴ 10
4
votes
8
replies
2.2k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2
limma
Normalization
R
updated 11 months ago by
Gordon Smyth
50k • written 17 months ago by
Sabiha
▴ 20
0
votes
8
replies
356
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 13 days ago by
swbarnes2
★ 1.3k • written 14 days ago by
Aaliya
• 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
0
votes
8
replies
1.2k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 5 months ago by
yw24418
• 0 • written 14 months ago by
sandra.garces.19
• 0
6
votes
8
replies
1.2k
views
CAGEr bug report: wrong consensus cluster results
CAGEr
updated 9 months ago by
Charles Plessy
▴ 180 • written 17 months ago by
Meng
▴ 30
0
votes
8
replies
646
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago
Marianna
▴ 20
3
votes
8
replies
916
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 5 months ago by
pcantalupo
▴ 10
0
votes
8
replies
717
views
Deseq2 Results are different using batch design
DESeq2
9 months ago
hemantcnaik
• 0
0
votes
8
replies
413
views
DESeq and SVA for batch effect
DESeq2
BatchEffect
sva
8 weeks ago
michelafrancesconi8
• 0
2
votes
8
replies
1.1k
views
Failure of beta estimates to converge in DESeq2 despite noncollinearity and reasonable counts
converge
beta
DESeq2
11 months ago • updated 10 months ago
Ndimensional
▴ 20
1
vote
8
replies
2.8k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.2 years ago by
serpalma.v
▴ 60
0
votes
8
replies
824
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression
DESeq2
6 months ago
Luca
• 0
0
votes
8
replies
1.7k
views
flowset/ncdfFlowset replace keywords doesn't work right
ncdfFlow
flowCore
updated 7 months ago by
osayou
• 0 • written 3.6 years ago by
anders.tondell
▴ 30
0
votes
8
replies
1.1k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray
TileDBArray
8 months ago • updated 7 months ago
sandmann.t
▴ 70
0
votes
8
replies
1.4k
views
Question about filterByExpr function edgeR
edgeR
8 months ago
lucap
• 0
1
vote
8
replies
551
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
2
votes
8
replies
1.3k
views
Reading GFF file and pre-processing, run iinfer_syntenet(), input and output
syntenet
updated 4 months ago by
Sujeevan
• 0 • written 16 months ago by
lwanderson8c
• 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
3
votes
8
replies
523
views
Constrast for Time Course Experiments using Limma
limma
9 weeks ago • updated 8 weeks ago
dl17032000
• 0
0
votes
8
replies
8.6k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 5 months ago by
Marcel Ramos
690 • written 2.8 years ago by
charlotte
▴ 10
4
votes
8
replies
1.2k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
11 months ago
Habil Zare
▴ 200
1
vote
8
replies
1.6k
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
8
votes
8
replies
9.8k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2
DESeq2
updated 7 months ago by
jd774
• 0 • written 4.8 years ago by
krassowski.michal
▴ 40
1
vote
8
replies
1.3k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 5 weeks ago by
Wolfgang Huber
★ 13k • written 10 months ago by
Jane
▴ 10
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago
Luis
• 0
3
votes
8
replies
528
views
Downloading package mixOmics
mixOmics
10 weeks ago
noortje_bloem94
• 0
0
votes
8
replies
714
views
GOslim missing GO term
GO.db
GOslim
5 months ago
amanda
• 0
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
written 21 months ago by
bpshtiwan
▴ 10
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2
RNASeq
updated 4 months ago by
Jon
• 0 • written 3.3 years ago by
Archit
▴ 10
1
vote
8
replies
1.5k
views
News:
Final List of Deprecated Package Bioc 3.9
deprecation
release
software
experimentData
News
written 5.1 years ago by
shepherl
3.9k
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 15 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
3
votes
7
replies
886
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
8 months ago
casco
▴ 10
1
vote
7
replies
4.5k
views
Problems Installing biomaRt
biomaRt
updated 5 months ago by
James W. MacDonald
65k • written 2.1 years ago by
ksci
▴ 20
0
votes
7
replies
1.6k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
BioES
• 0
8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by
Daniel E. Weeks
▴ 30
1,749 results • Page
3 of 35
Recent ...
Replies
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results
by
ATpoint
★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data
by
ATpoint
★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
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