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1
vote
7
replies
331
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
12 days ago • updated 11 days ago
pl23
• 0
2
votes
9
replies
394
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 12 days ago by
Alexandre
• 0
0
votes
0
replies
129
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
12 days ago • updated 4 days ago
glaciya2018
• 0
0
votes
2
replies
214
views
PCA plot suggestions
DESeq2
PCAtools
updated 11 days ago by
Michael Love
42k • written 13 days ago by
Aaliya
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 13 days ago by
Michael Love
42k • written 13 days ago by
kcarey
• 0
0
votes
1
reply
140
views
ATACseq merge peaks
DiffBind
updated 11 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Shloka
• 0
0
votes
0
replies
90
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
13 days ago • updated 8 days ago
Sara
• 0
0
votes
0
replies
85
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
13 days ago
Dario Strbenac
★ 1.5k
1
vote
2
replies
161
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
13 days ago • updated 12 days ago
ATpoint
★ 4.1k
1
vote
3
replies
216
views
Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
336
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago
winwater0928
• 0
2
votes
5
replies
276
views
get BM error
ensembldb
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Fara
• 0
2
votes
5
replies
245
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 12 days ago by
James W. MacDonald
65k • written 14 days ago by
bandconductor
• 0
1
vote
1
reply
179
views
Citation for edgeR user guide
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 14 days ago by
k___
▴ 30
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by
Michael Love
42k • written 14 days ago by
i.sudbery
▴ 40
1
vote
1
reply
116
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
fernanda.backsouza
▴ 10
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
0
votes
0
replies
73
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
14 days ago
info
▴ 10
0
votes
2
replies
251
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
15 days ago • updated 12 days ago
shuwangxinze1996
• 0
0
votes
2
replies
170
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 15 days ago by
taur.vil
• 0
3
votes
3
replies
231
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by
Michael Love
42k • written 15 days ago by
WardDeb
• 0
1
vote
4
replies
210
views
minfi::read.metharray.exp
minfiData
minfi
updated 13 days ago by
Basti
▴ 780 • written 15 days ago by
clacarion
• 0
1
vote
2
replies
191
views
Improving the design matrices vignette in RNAseq123
RNAseq123
15 days ago • updated 1 day ago
Lluís Revilla Sancho
▴ 730
0
votes
5
replies
303
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 13 days ago by
James W. MacDonald
65k • written 16 days ago by
Gayatri
• 0
2
votes
13
replies
432
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
16 days ago • updated 13 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
84
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
16 days ago
vaxahey107
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
17 days ago • updated 6 days ago
Chris
• 0
0
votes
0
replies
100
views
I am trying to detect alternative splicing.
ASpli
17 days ago
Sebashish
• 0
3
votes
2
replies
217
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 15 days ago by
Guido Hooiveld
★ 3.9k • written 18 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
128
views
FDR via q-value
qvalue
updated 15 days ago by
James W. MacDonald
65k • written 18 days ago by
John
• 0
0
votes
2
replies
215
views
RNAseq:Technical replicates from different batches
technicalReplicates
BatchEffect
limma
RNASeq
18 days ago • updated 15 days ago
catv
• 0
0
votes
3
replies
156
views
Error retrieving ensembl gene id using biomaRt...
biomaRt
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
bas_work
▴ 30
1
vote
0
replies
290
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor
Install
18 days ago
BioinfGuru
▴ 30
0
votes
2
replies
138
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
18 days ago
prity6459
• 0
2
votes
2
replies
193
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 18 days ago by
James W. MacDonald
65k • written 19 days ago by
sansan
• 0
0
votes
4
replies
207
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
19 days ago
sropri
• 0
1
vote
4
replies
240
views
Error EPICv2 ChAMP
ChAMPdata
IlluminaHumanMethylationEPICv2anno.20a1.hg38
ChAMP
updated 15 days ago by
James W. MacDonald
65k • written 19 days ago by
Mirella Aurora
• 0
0
votes
3
replies
193
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
prity6459
• 0
0
votes
0
replies
122
views
Warning while loading DEP package
DEP
updated 19 days ago by
shepherl
3.9k • written 19 days ago by
Namrata
• 0
0
votes
3
replies
174
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 19 days ago by
Alessia
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
ishij9717
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 19 days ago by
Michael Love
42k • written 19 days ago by
09191919
• 0
3
votes
1
reply
179
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
Shaimaa Gamal
• 0
1
vote
2
replies
221
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
19 days ago
Le
• 0
1
vote
2
replies
160
views
Error in champ.load(): The following specified files do not exist
ChAMP
20 days ago • updated 19 days ago
Sherin
• 0
0
votes
1
reply
101
views
Input Question for deseq.r
RSeqAn
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
Nina
• 0
4
votes
6
replies
438
views
FilterByExpr low counts with small sample size
edgeR
20 days ago • updated 15 days ago
Jonathan
▴ 10
0
votes
4
replies
241
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
20 days ago • updated 17 days ago
lonn
• 0
1
vote
2
replies
719
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago
ussarizona
▴ 10
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
quanah.hudson
• 0
45,629 results • Page
2 of 913
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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