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0
votes
2
replies
1.3k
views
ape::dnds produces nan value
R
ape
dnds
nan
nanotubes
3.1 years ago
Working
• 0
0
votes
2
replies
2.4k
views
Getting this error while trying to use edgeR "Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any'"
edgeR
edge
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
Isa
• 0
2
votes
1
reply
1.5k
views
How to interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
Pratik Mehta
▴ 10
0
votes
2
replies
1.6k
views
Deseq2 and co-expression network normalization
DESeq2
Normalization
DifferentialExpression
r
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
lola
• 0
0
votes
1
reply
775
views
DESeq2, normalization for within-sample comparison, and 3'-end RNAseq data
DESeq2
updated 3.1 years ago by
Michael Love
43k • written 3.2 years ago by
theophile
• 0
0
votes
1
reply
1.6k
views
unable to load edgeR after installing it
edgeR
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Vittorio
• 0
0
votes
3
replies
2.3k
views
GDCprepare : Error: BiocParallel errors/Error in stopAndCache(title):
BiocParallelerrors
updated 23 months ago by
Siri
• 0 • written 3.2 years ago by
shuangshuang
• 0
4
votes
2
replies
2.3k
views
DESeq2 false positive result?
DESeq2
updated 3.1 years ago by
swbarnes2
★ 1.4k • written 3.1 years ago by
Gregor
▴ 10
1
vote
2
replies
1.5k
views
Changing the sample order in the PCA plot
DESeq2
3.1 years ago
turtle888
• 0
0
votes
2
replies
1.5k
views
Remove low-expressed genes in DESeq2?
DESeq2
lowcountgenes
deseq2
independent
written 3.1 years ago by
erbrocato
• 0
2
votes
4
replies
6.1k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2
R
edgeR
Normalization
RNASeq
3.1 years ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
824
views
coexpression networks
WGCNA
igraph
3.1 years ago
María José
• 0
0
votes
0
replies
949
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
3.1 years ago
Abdullah
• 0
1
vote
7
replies
2.5k
views
query regarding error in installation of "goseq" R bioconductor package
R
Bioconductor
Install
updated 3.1 years ago by
shepherl
4.3k • written 3.1 years ago by
abhisek001
• 0
1
vote
3
replies
2.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 3.1 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Arctic
• 0
0
votes
3
replies
1.3k
views
IHW for multiple regression
IHW
updated 3.0 years ago by
Wolfgang Huber
★ 13k • written 3.1 years ago by
Tyson
• 0
0
votes
1
reply
807
views
NA value in padj but only for certain contrasts
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Yiqi
▴ 10
1
vote
12
replies
3.9k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2
edgeR
limma
updated 3.1 years ago by
Michael Love
43k • written 3.2 years ago by
Bogdan
▴ 670
0
votes
1
reply
761
views
DESeq2 : Using contrast in results vs performing complete independent analysis
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
andree-anne
• 0
0
votes
2
replies
1.4k
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2
adjp
Volcano
LRT
written 3.2 years ago by
Laia
▴ 10
0
votes
1
reply
1.3k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2
interaction
coefficient
LinearModel
RNASeq
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Pedro Milanez-Almeida
▴ 10
0
votes
1
reply
938
views
Design structure
DESeq2
des
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Devin
• 0
1
vote
2
replies
1.3k
views
Question about contrasts in DESeq2
DESeq2
3.2 years ago • updated 3.1 years ago
marinaw
▴ 20
0
votes
1
reply
1.2k
views
Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2
time-series
timecoursedata
timecourse
multifactorial
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
arshad1292
• 0
0
votes
1
reply
902
views
Strange dispersion plot with high outliers
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
mary.piper
• 0
0
votes
1
reply
1.0k
views
How to extract DeSeq2 results for the different groups?
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Itsme
• 0
0
votes
1
reply
870
views
DESeq2 paired multifactor test
DESeq2
StatisticalMethod
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
ijvechetti
▴ 10
0
votes
0
replies
1.0k
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 3.1 years ago by
Michael Love
43k • written 3.2 years ago by
barrypraveen
• 0
1
vote
3
replies
1.2k
views
Older source of biocFileCache package
biomaRt
updated 3.2 years ago by
Mike Smith
★ 6.6k • written 3.2 years ago by
julian.konzok
• 0
1
vote
3
replies
1.8k
views
Problem with DESeq2
DESeq2
apple-m1
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Norbert
▴ 10
0
votes
1
reply
922
views
Empty ChipQC Report
ChipQCReport
updated 3.0 years ago by
Okan
• 0 • written 3.2 years ago by
stacy.genovese
• 0
1
vote
3
replies
1.9k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR
voom
normalization
DifferentialExpression
updated 3.1 years ago by
Gordon Smyth
53k • written 3.2 years ago by
wiscoyogi
• 0
1
vote
1
reply
4.0k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Sara
• 0
0
votes
2
replies
1.5k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq
ChIPSeqData
chipseqDB
3.2 years ago
stacy.genovese
• 0
0
votes
4
replies
1.5k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2
RNASeq
PrincipalComponent
pcaExplorer
written 3.2 years ago by
James
• 0
0
votes
3
replies
1.7k
views
Difficulty creating summarized experiment
sesame
sesameData
updated 3.2 years ago by
zhouwanding
▴ 20 • written 3.2 years ago by
jasmine_chappell
• 0
0
votes
2
replies
1.4k
views
Error received in ropls package
Metabolomics
ropls
updated 3.2 years ago by
etienne.thevenot
▴ 40 • written 3.2 years ago by
ansari.maya022
• 0
1
vote
3
replies
7.6k
views
Not able to install packages in Bioconductor version '3.16'
Install
BiocManager
version3.16
updated 3.0 years ago by
shepherl
4.3k • written 3.2 years ago by
Tonmoya
• 0
1
vote
5
replies
1.6k
views
how can I add a label for granges using the geom_rect ?
ggbio
3.2 years ago
潘晓光
• 0
0
votes
1
reply
1.8k
views
DESeq2 design function and downstream analyses
DESeq2
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Devin
• 0
6
votes
6
replies
2.3k
views
Too many differentially expressed miRNA with limma
limma
miRNA
Microarray
3.2 years ago
Sara
▴ 20
0
votes
2
replies
1.3k
views
Filtering normalised counts
DESeq2
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Rob
• 0
1
vote
1
reply
2.7k
views
Instaling glmGamPoi
glmGamPoi
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.2 years ago by
sina.tadayon
• 0
1
vote
1
reply
1.1k
views
ggcyto::scale_x_logicle() not converging
ggcyto
updated 3.1 years ago by
shepherl
4.3k • written 3.2 years ago by
philippe.hauchamps
▴ 10
1
vote
1
reply
1.5k
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 3.2 years ago by
Gordon Smyth
53k • written 3.2 years ago by
Brian
• 0
1
vote
2
replies
2.5k
views
object of type 'externalptr' is not subsettable in R4.0 - with COM Object
r4.0
ComponentObjectModel
subsetting
3.2 years ago
Duy Duc
• 0
0
votes
0
replies
994
views
Job:
Post Doctoral Research Officer - Bioinformatics
JobPosting
3.2 years ago
hdawson
• 0
2
votes
3
replies
3.2k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal
ensembldb
rtracklayer
Annotation
updated 3.0 years ago by
rbj
• 0 • written 3.2 years ago by
Jake
▴ 10
0
votes
1
reply
1.6k
views
How to remove INDELS/SNPs from a bed file
SNP
updated 3.2 years ago by
James W. MacDonald
68k • written 3.2 years ago by
Cian
• 0
0
votes
0
replies
1.5k
views
WGCNA: minModuleSize is not responding correctly
Network
minModuleSize
WGCNA
wgcna
3.2 years ago • updated 16 months ago
bioinformaticssrm2011
• 0
46,727 results • Page
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Answer: Are individual-mouse-based statistics possible in CellChat?
by
ATpoint
★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups
by
ATpoint
★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Martin Morgan
25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Benjamin
• 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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