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2
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7
replies
3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 8 months ago by
lucap
• 0 • written 3.0 years ago by
Marianna
▴ 20
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 22 days ago
shepherl
3.9k
1
vote
7
replies
2.9k
views
Technical details of DiffBind correlation analysis
diffbind
duplicatecorrelation
updated 3 months ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
meisan406
• 0
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression
proteomics
updated 8 months ago by
ATpoint
★ 4.1k • written 6.3 years ago by
cardin.julie
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 4 days ago
Henrik Bengtsson
★ 2.4k
0
votes
11
replies
2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by
James W. MacDonald
65k • written 20 months ago by
ignadb
• 0
1
vote
2
replies
2.8k
views
TPM to raw counts
salmon
DESeq2
updated 5 months ago by
bella.johnson.2022
• 0 • written 2.3 years ago by
Sneha
• 0
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by
Michael Love
42k • written 2.5 years ago by
nicolette.sipperly
• 0
3
votes
10
replies
2.8k
views
error in package GenVisR while installing
GenVisR
GenVis
updated 6 months ago by
zlskidmore
▴ 30 • written 21 months ago by
abhisikta
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 7 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
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
3
replies
2.8k
views
Error: BiocParallel errors 1 remote errors, element index: 1 506 unevaluated and other errors first remote error:
methylationArrayAnalysis
updated 9 months ago by
olatunbosun.arowolo
• 0 • written 18 months ago by
shuangshuang
• 0
1
vote
12
replies
2.8k
views
How to use "p-value" instead of "p-adj value" in DESeq2
DESeq2
updated 6 months ago by
Assa Yeroslaviz
★ 1.5k • written 22 months ago by
Maryam.sed1400
• 0
7
votes
4
replies
2.8k
views
Normalized counts of DESeq2 affected by design formula?
deseq2
updated 4 months ago by
Garrett
• 0 • written 6.2 years ago by
blastzone.heimerdinger
▴ 20
0
votes
39
replies
2.8k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
15 months ago • updated 9 hours ago
Poonam
• 0
3
votes
6
replies
2.8k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 11 weeks ago by
Dinesh
• 0 • written 5.3 years ago by
Ben
▴ 50
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by
Gordon Smyth
50k • written 12.0 years ago by
Kripa R
▴ 180
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.1 years ago by
Colari19
▴ 60
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.5 years ago by
Camila Orellana
▴ 10
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
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
2
replies
2.6k
views
How to get the rsID of 4 million SNPA
ensembldb
SNP
SNPData
genomes
written 2.2 years ago by
Weiqiong
• 0
2
votes
2
replies
2.6k
views
After having the output from SingleR for cell type annotation, what's the next step to assign the cell type to each cluster
SingleCellSignalR
SingleCellWorkflow
SingleR
updated 5 months ago by
Assa Yeroslaviz
★ 1.5k • written 3.0 years ago by
FantasticAI
▴ 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 3.4 years ago by
Archit
▴ 10
1
vote
4
replies
2.6k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 17 months ago by
Sarah
• 0
8
votes
12
replies
2.6k
views
DESeq2 1.40.0 binary install issue on macOS x86 (Bioconductor 3.17)
DESeq2
updated 12 months ago by
Michael Love
42k • written 12 months ago by
Michael Steinbaugh
▴ 90
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 11 months ago by
Aung
• 0 • written 14 months ago by
pedro-marra
▴ 10
2
votes
6
replies
2.6k
views
Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TRUE/FALSE needed
software error
cn.mops
updated 8 weeks ago by
ama304374
• 0 • written 6.3 years ago by
daijieqiong
▴ 10
0
votes
18
replies
2.5k
views
problem installing ENmix package
ENmix
Bioconductor
rtracklayer
written 3.2 years ago by
lea
• 0
3
votes
11
replies
2.5k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq
mixedmodels
baselineadjustement
limma
11 months ago
Anna
▴ 20
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 9 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
2.5k
views
How to handle BSsmooth.tstat for single replicate samples? Error: need at least two non-NA values to interpolate
bsseq
Bsmooth
updated 6 months ago by
Adam
• 0 • written 9.2 years ago by
unmeshj
• 0
0
votes
3
replies
2.5k
views
Background correction with neqc
Normalization
Cancer
Normalization
Cancer
updated 6 months ago by
Gordon Smyth
50k • written 12.4 years ago by
Guest User
★ 13k
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
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 6 months ago by
blowfish
• 0 • written 6.5 years ago by
bharata1803
▴ 60
0
votes
1
reply
2.5k
views
Warning messages in detecting P-values
minfiDataEPIC
methylationArrayAnalysis
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
rae.alshammari
▴ 10
0
votes
2
replies
2.5k
views
vmatchPattern on DNAstring set
Bioconductor
9 months ago
Avner
• 0
2
votes
7
replies
2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray
methylationArrayAnalysis
ChAMP
updated 7 months ago by
dorota.komar
• 0 • written 3.4 years ago by
Ankit
▴ 20
1
vote
12
replies
2.4k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma
highthroughputassays
R
updated 3 months ago by
Mary
• 0 • written 2.5 years ago by
Ming
▴ 380
2
votes
2
replies
2.4k
views
Biostatistician Position: UMass Medical School
Microarray
Microarray
written 16.8 years ago by
David Lapointe
▴ 190
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
0
votes
3
replies
2.4k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm
LEA
updated 6 weeks ago by
m.charters
• 0 • written 3.0 years ago by
valentinarov
• 0
4
votes
6
replies
2.3k
views
DESeq2 for single cell pseudobulk processing
DESeq2
updated 12 months ago by
Michael Love
42k • written 13 months ago by
r2626
• 0
0
votes
2
replies
2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 8 months ago by
manuel.fernandez
• 0 • written 2.1 years ago by
cicely.day
• 0
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
0
votes
5
replies
2.3k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts
SAM
htseqcounts
updated 10 months ago by
Yang Liao
▴ 380 • written 7.0 years ago by
courtney.stairs
• 0
1
vote
1
reply
2.3k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 9 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
bhandary.8590
▴ 20
2
votes
2
replies
2.2k
views
ComplexHeatmap: Change font size of annotation axis values
ComplexHeatmap
updated 9 months ago by
franciscaelibethgalvez
• 0 • written 22 months ago by
nalaspina
▴ 10
0
votes
10
replies
2.2k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR
rna-seq
splice-variants
written 5.1 years ago by
saddamhusain77
• 0
3
votes
1
reply
2.2k
views
Tutorial:
Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry
proteomics
metabolomics
Tutorial
written 3.6 years ago by
Johannes Rainer
★ 2.0k
1,745 results • Page
3 of 35
Recent ...
Replies
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go! And for comparisons between the cohorts I presume duplicateCorrelation with standar…
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Comment: Extremely small p-values using Limma for proteomic data
by
Abbey
• 0
This is the code. The only part I changed was adding the contrasts.fit as you suggested. Thanks for taking a look! ``` # Load necessary …
Comment: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
Probably. I would not expect such large fold changes. But without seeing your code, who knows?
Votes
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
Bioconductor 3.19 is Released!
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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