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0
votes
0
replies
11
views
FDR via q-value
qvalue
1 hour ago
John
• 0
0
votes
0
replies
13
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
4 hours ago
catv
• 0
0
votes
0
replies
24
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
1 day ago
Mirella Aurora
• 0
0
votes
0
replies
36
views
Warning while loading DEP package
DEP
updated 1 day ago by
shepherl
3.8k • written 1 day ago by
Namrata
• 0
1
vote
2
replies
132
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
1 day ago • updated 23 hours ago
Le
• 0
1
vote
2
replies
85
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 day ago
Sherin
• 0
0
votes
1
reply
53
views
Input Question for deseq.r
RSeqAn
updated 1 day ago by
ATpoint
★ 4.0k • written 2 days ago by
Nina
• 0
0
votes
3
replies
107
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 11 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
0
replies
30
views
Enzyme Engineering
BioTIP
2 days ago
bocchemistry
• 0
0
votes
0
replies
48
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
3 days ago • updated 2 days ago
Maliha Tabassum
• 0
0
votes
1
reply
73
views
what is the sampleFiles
chipseq
updated 3 days ago by
James W. MacDonald
65k • written 3 days ago by
zhulin
• 0
0
votes
0
replies
59
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
3 days ago
Virangika
• 0
0
votes
0
replies
43
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 days ago
Henry
▴ 10
0
votes
1
reply
94
views
Deseq2 Rlog transformation
DESeq2
updated 4 days ago by
ATpoint
★ 4.0k • written 5 days ago by
Sahar
• 0
2
votes
2
replies
135
views
[DiffBind] Obtaining normalization factors
DiffBind
7 days ago • updated 3 days ago
Henry
▴ 10
0
votes
3
replies
190
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 1 day ago by
W. Evan Johnson
▴ 850 • written 7 days ago by
schlumbohm
• 0
0
votes
0
replies
68
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
7 days ago
Stevie Pederson
• 0
3
votes
6
replies
209
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
8 days ago
nhaus
▴ 30
0
votes
1
reply
141
views
DESeq2 gives an error and R crashes
DESeq2
8 days ago • updated 7 days ago
Shefali
• 0
0
votes
0
replies
100
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
8 days ago
Eryn
• 0
0
votes
0
replies
68
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
9 days ago
Dennis
• 0
0
votes
1
reply
111
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 days ago by
Guido Hooiveld
★ 3.9k • written 9 days ago by
Lucie
• 0
0
votes
0
replies
81
views
ggtree tip label position (depth)
ggtree
10 days ago • updated 9 days ago
Roope
• 0
2
votes
6
replies
309
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
11 days ago • updated 10 days ago
Chris
• 0
0
votes
0
replies
122
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
14 days ago
andromeda
• 0
0
votes
1
reply
108
views
Granges regionCounts not returning the expected number of entries
methylKit
14 days ago • updated 13 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
77
views
flowDensity on a flowset
flowDensity
14 days ago
fredrikwallberg
• 0
0
votes
0
replies
70
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
15 days ago
Macsue
• 0
0
votes
1
reply
126
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
ja569116
• 0
0
votes
2
replies
261
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
18 days ago • updated 14 days ago
fer_talavera
• 0
0
votes
2
replies
209
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
19 days ago • updated 4 hours ago
isaac.vock
• 0
0
votes
7
replies
321
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
20 days ago • updated 17 days ago
needNGS
• 0
0
votes
0
replies
93
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 days ago
feather-W
• 0
0
votes
0
replies
91
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 days ago
Ankit
▴ 20
1
vote
5
replies
287
views
fgsea fork
fgsea
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
yimjohns
• 0
0
votes
0
replies
78
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
22 days ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
334
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 25 days ago by
alan.ocallaghan
▴ 160 • written 26 days ago by
Najla Abassi
• 0
0
votes
0
replies
97
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
25 days ago
gshweta95
• 0
2
votes
1
reply
176
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 26 days ago by
Guido Hooiveld
★ 3.9k • written 28 days ago by
enee
▴ 10
0
votes
0
replies
99
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
28 days ago
nromerov
• 0
1
vote
3
replies
230
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 28 days ago by
Marcel Ramos
690 • written 29 days ago by
Astrid Deschênes
• 0
0
votes
0
replies
107
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
29 days ago
mayra.haedo
• 0
0
votes
0
replies
100
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
4 weeks ago
taylor.witte
• 0
0
votes
0
replies
119
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
4 weeks ago
erbrocato
• 0
1
vote
4
replies
249
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
4 weeks ago • updated 29 days ago
samuel.channon
• 0
0
votes
2
replies
181
views
Visium RNA
metaMSdata
updated 4 weeks ago by
vvvc360work2
• 0 • written 4 weeks ago by
Karlison
• 0
1
vote
2
replies
242
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 4 weeks ago by
ATpoint
★ 4.0k • written 4 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
103
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
4 weeks ago
BID
• 0
1
vote
3
replies
245
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 22 days ago by
mercedeh.movassagh
▴ 10 • written 4 weeks ago by
María
• 0
0
votes
2
replies
192
views
Error in msaFun Cannot open input file. No alignment!
msa
written 4 weeks ago by
Kamil Slowikowski
▴ 30
1,000 results • Page
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Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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