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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
9 days ago • updated 7 days ago
shuwangxinze1996
• 0
0
votes
2
replies
150
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
3
votes
3
replies
213
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by
Michael Love
41k • written 10 days ago by
WardDeb
• 0
1
vote
4
replies
195
views
minfi::read.metharray.exp
minfiData
minfi
updated 8 days ago by
Basti
▴ 780 • written 10 days ago by
clacarion
• 0
1
vote
1
reply
151
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
285
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 8 days ago by
James W. MacDonald
65k • written 11 days ago by
Gayatri
• 0
1
vote
13
replies
369
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 8 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
76
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
11 days ago
vaxahey107
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
0
votes
0
replies
90
views
I am trying to detect alternative splicing.
ASpli
12 days ago
Sebashish
• 0
3
votes
2
replies
204
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 10 days ago by
Guido Hooiveld
★ 3.9k • written 13 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
119
views
FDR via q-value
qvalue
updated 10 days ago by
James W. MacDonald
65k • written 13 days ago by
John
• 0
0
votes
2
replies
195
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
13 days ago • updated 10 days ago
catv
• 0
0
votes
3
replies
139
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
bas_work
▴ 30
1
vote
0
replies
263
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
13 days ago
BioinfGuru
▴ 30
0
votes
2
replies
123
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 days ago
prity6459
• 0
2
votes
2
replies
178
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
sansan
• 0
0
votes
4
replies
187
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
14 days ago
sropri
• 0
1
vote
4
replies
215
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 10 days ago by
James W. MacDonald
65k • written 14 days ago by
Mirella Aurora
• 0
0
votes
3
replies
178
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
prity6459
• 0
0
votes
0
replies
114
views
Warning while loading DEP package
DEP
updated 14 days ago by
shepherl
3.9k • written 14 days ago by
Namrata
• 0
0
votes
3
replies
154
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Alessia
• 0
0
votes
1
reply
123
views
rlog transformation
DESeq2
updated 14 days ago by
Michael Love
41k • written 14 days ago by
ishij9717
• 0
0
votes
1
reply
105
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 14 days ago by
Michael Love
41k • written 14 days ago by
09191919
• 0
3
votes
1
reply
160
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
207
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 days ago
Le
• 0
1
vote
2
replies
150
views
Error in champ.load(): The following specified files do not exist
ChAMP
15 days ago • updated 14 days ago
Sherin
• 0
0
votes
1
reply
97
views
Input Question for deseq.r
RSeqAn
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Nina
• 0
4
votes
6
replies
400
views
FilterByExpr low counts with small sample size
edgeR
15 days ago • updated 10 days ago
Jonathan
▴ 10
0
votes
4
replies
229
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 12 days ago
lonn
• 0
1
vote
2
replies
694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago
ussarizona
▴ 10
0
votes
1
reply
138
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
quanah.hudson
• 0
0
votes
7
replies
290
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
15 days ago • updated 9 days ago
hortense96
• 0
0
votes
0
replies
73
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flowBeads
15 days ago
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• 0
0
votes
1
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128
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covariate with negative and positive values
DESeq2
updated 14 days ago by
Michael Love
41k • written 16 days ago by
Brynn
• 0
0
votes
1
reply
147
views
Adding columns to DEXSeqResults object
DEXSeq
updated 14 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Clyde
• 0
0
votes
0
replies
88
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
16 days ago
Maliha Tabassum
• 0
1
vote
2
replies
131
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
16 days ago
Ana
• 0
0
votes
1
reply
118
views
what is the sampleFiles
chipseq
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
zhulin
• 0
0
votes
4
replies
182
views
flowStats Search Error
flowStats
updated 16 days ago by
shepherl
3.9k • written 17 days ago by
tholmes
• 0
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
17 days ago
Virangika
• 0
0
votes
0
replies
70
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 days ago
Henry
▴ 10
0
votes
3
replies
200
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by
Michael Love
41k • written 17 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
319
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago
daniel.carbajo
• 0
0
votes
4
replies
260
views
DEG with low counts
DESeq2
updated 13 days ago by
Michael Love
41k • written 18 days ago by
Rajat
• 0
1
vote
2
replies
484
views
GSVA error
GSVA
18 days ago • updated 17 days ago
Alex
• 0
0
votes
1
reply
128
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
1
vote
1
reply
182
views
Differentially expressed genes in monocle pseudotime
monocle
updated 16 days ago by
Gordon Smyth
50k • written 18 days ago by
kthapa
• 0
1,000 results • Page
2 of 20
Recent ...
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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