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0
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4
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94
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all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
16 hours ago • updated 6 hours ago
Galina
• 0
0
votes
0
replies
14
views
LRT, more than two conditions and pairwise comparisons
DESeq2
7 hours ago
boczniak767
▴ 720
0
votes
0
replies
14
views
How to run allelic imbalance in apeglm
apeglm
8 hours ago
euge.eugenio
▴ 20
7
votes
5
replies
560
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
14 days ago • updated 8 hours ago
robersy
• 0
0
votes
4
replies
430
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
2 days ago • updated 8 hours ago
Ken C
• 0
0
votes
1
reply
63
views
Subsetting RNAseq data | voomaByGroup()
limma
updated 13 hours ago by
Gordon Smyth
50k • written 1 day ago by
Anna
• 0
0
votes
0
replies
22
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
14 hours ago • updated 13 hours ago
Bibi
• 0
0
votes
0
replies
37
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
1 day ago • updated 16 hours ago
Abiologist
• 0
0
votes
0
replies
33
views
ERROR; return code from pthread_create() is 22
affy
1 day ago • updated 17 hours ago
pickingastar
• 0
0
votes
2
replies
116
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
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 2 days ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
0
votes
3
replies
106
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
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 2 days ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
2
votes
5
replies
218
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
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 2 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
1
vote
2
replies
246
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
6 days ago • updated 3 days ago
BioinfGuru
▴ 30
0
votes
2
replies
113
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
3 days ago
makala
• 0
2
votes
2
replies
388
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
8 days ago • updated 3 days ago
Matthew Thornton
▴ 360
0
votes
0
replies
52
views
determine k during RUVSeq
RUVSeq
RUVnormalize
3 days ago
Ειρήνη
• 0
4
votes
9
replies
256
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
2
votes
3
replies
106
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
52
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
71
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
3 days ago
Anton01
• 0
10
votes
10
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 3 days ago by
Leonard Goldstein
▴ 220 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
0
replies
46
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
4 days ago
danalvoronov
▴ 10
0
votes
0
replies
45
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
4 days ago
k200987
• 0
2
votes
3
replies
126
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 4 days ago by
Gordon Smyth
50k • written 4 days ago by
Guillermo
• 0
0
votes
2
replies
752
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 4 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
4
replies
132
views
error running enricher from clusterprofiler
clusterProfiler
cluster
4 days ago
Yael
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 4 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
1
vote
2
replies
132
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
5 days ago • updated 4 days ago
Daniel
• 0
4
votes
5
replies
328
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
14 days ago • updated 4 days ago
Chris
▴ 10
0
votes
2
replies
951
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 4 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
2
votes
1
reply
74
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
117
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
98
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
4 days ago
Patadù
▴ 10
0
votes
0
replies
40
views
Difference in Contrast in DiffBind
DiffBind
4 days ago
zzrammal
• 0
1
vote
2
replies
204
views
Citation for edgeR user guide
edgeR
written 26 days ago by
k___
▴ 30
1
vote
3
replies
249
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 5 days ago by
Gordon Smyth
50k • written 6 days ago by
Ashley
• 0
0
votes
8
replies
507
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 5 days ago by
BioinfGuru
▴ 30 • written 6 days ago by
Eric Katagirya
• 0
0
votes
2
replies
133
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 5 days ago by
zhouwanding
▴ 10 • written 7 days ago by
Seungmin
• 0
1
vote
0
replies
333
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 5 days ago
shepherl
3.9k
0
votes
2
replies
104
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
6 days ago • updated 5 days ago
Yveto
• 0
0
votes
1
reply
97
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
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 5 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
1
vote
0
replies
64
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
5 days ago
Aleena
▴ 30
0
votes
3
replies
183
views
ChAMP installation issue
Cha
ChAMP
6 days ago • updated 5 days ago
e1271094
• 0
0
votes
0
replies
57
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
5 days ago
Researcher
• 0
3
votes
4
replies
287
views
Store output of matchPWM()
biostrings
Biostrings
18 days ago • updated 6 days ago
mat149
▴ 70
1,000 results • Page
1 of 20
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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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