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0
votes
0
replies
7
views
LRT, more than two conditions and pairwise comparisons
DESeq2
1 hour ago
boczniak767
▴ 720
0
votes
0
replies
10
views
How to run allelic imbalance in apeglm
apeglm
1 hour ago
euge.eugenio
▴ 20
0
votes
0
replies
18
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
8 hours ago • updated 7 hours ago
Bibi
• 0
0
votes
4
replies
59
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
10 hours ago • updated 21 minutes ago
Galina
• 0
0
votes
1
reply
57
views
Subsetting RNAseq data | voomaByGroup()
limma
updated 6 hours ago by
Gordon Smyth
50k • written 1 day ago by
Anna
• 0
0
votes
0
replies
31
views
ERROR; return code from pthread_create() is 22
affy
1 day ago • updated 11 hours ago
pickingastar
• 0
0
votes
0
replies
36
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
1 day ago • updated 10 hours ago
Abiologist
• 0
0
votes
2
replies
111
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 1 day ago by
Michael Love
42k • written 2 days ago by
shaunpeterson
• 0
0
votes
3
replies
100
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 2 days ago by
damian.szk
▴ 80 • written 2 days ago by
ninidea
• 0
0
votes
4
replies
377
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
2 days ago • updated 2 hours ago
Ken C
• 0
0
votes
2
replies
110
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
3 days ago
makala
• 0
0
votes
0
replies
50
views
determine k during RUVSeq
RUVSeq
RUVnormalize
3 days ago
Ειρήνη
• 0
0
votes
0
replies
50
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
3 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
3 days ago
oliverelijhan
0
0
votes
0
replies
68
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
3 days ago
Anton01
• 0
2
votes
3
replies
104
views
Problem installing ChAMP on a MacBook
ChAMP
updated 3 days ago by
shepherl
3.9k • written 3 days ago by
Galia
• 0
0
votes
0
replies
45
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
3 days ago
danalvoronov
▴ 10
0
votes
0
replies
40
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
3 days ago
k200987
• 0
2
votes
5
replies
215
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
4 days ago • updated 2 days ago
Patadù
▴ 10
0
votes
4
replies
130
views
error running enricher from clusterprofiler
clusterProfiler
cluster
4 days ago
Yael
• 0
2
votes
3
replies
124
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Guillermo
• 0
0
votes
0
replies
39
views
Difference in Contrast in DiffBind
DiffBind
4 days ago
zzrammal
• 0
4
votes
9
replies
252
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
pangtaihin
• 0
1
vote
2
replies
95
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
4 days ago
Patadù
▴ 10
0
votes
3
replies
113
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 4 days ago by
Michael Love
42k • written 5 days ago by
Kasper
• 0
1
vote
2
replies
128
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
5 days ago • updated 4 days ago
Daniel
• 0
1
vote
0
replies
62
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
5 days ago
Aleena
▴ 30
0
votes
0
replies
55
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
5 days ago
Researcher
• 0
1
vote
3
replies
248
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 4 days ago by
Gordon Smyth
50k • written 5 days ago by
Ashley
• 0
1
vote
2
replies
243
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
5 days ago • updated 3 days ago
BioinfGuru
▴ 30
0
votes
8
replies
502
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 4 days ago by
BioinfGuru
▴ 30 • written 6 days ago by
Eric Katagirya
• 0
0
votes
1
reply
95
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 5 days ago by
Michael Love
42k • written 6 days ago by
piemmea
• 0
0
votes
2
replies
103
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
6 days ago • updated 5 days ago
Yveto
• 0
2
votes
1
reply
72
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 4 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Sara
• 0
0
votes
3
replies
180
views
ChAMP installation issue
Cha
ChAMP
6 days ago • updated 5 days ago
e1271094
• 0
0
votes
1
reply
140
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 6 days ago by
Guido Hooiveld
★ 4.0k • written 7 days ago by
aogunbaw
• 0
0
votes
2
replies
130
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 5 days ago by
zhouwanding
▴ 10 • written 7 days ago by
Seungmin
• 0
2
votes
2
replies
382
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
7 days ago • updated 3 days ago
Matthew Thornton
▴ 360
0
votes
1
reply
170
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
0
votes
0
replies
80
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
9 days ago
neilzhao
▴ 30
0
votes
1
reply
108
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
1
vote
2
replies
272
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
10 days ago • updated 9 days ago
Dylan.Sheerin
• 0
2
votes
7
replies
388
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
11 days ago • updated 8 days ago
sajadahmad41454
• 0
0
votes
0
replies
75
views
Treeio as.treedata function seq lenght error
treeio
11 days ago
nromerov
• 0
2
votes
2
replies
279
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
12 days ago • updated 6 days ago
zzrammal
• 0
3
votes
10
replies
463
views
Extremely small p-values using Limma for proteomic data
Proteomics
limma
updated 9 days ago by
James W. MacDonald
65k • written 12 days ago by
Abbey
• 0
0
votes
1
reply
114
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 12 days ago by
shepherl
3.9k • written 12 days ago by
cyril.dalmasso
• 0
2
votes
1
reply
176
views
minfi latest update for EPIC V2 chip
minfi
minfiDataEPIC
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
e1271094
• 0
0
votes
0
replies
94
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 days ago
Dinesh
• 0
3
votes
5
replies
297
views
Help with running egsea()
EGSEA
13 days ago • updated 11 days ago
Chris
▴ 10
168 results • Page
1 of 4
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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