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all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
just now
Galina
• 0
0
votes
0
replies
32
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
1 day ago • updated 10 minutes ago
Abiologist
• 0
0
votes
0
replies
25
views
ERROR; return code from pthread_create() is 22
affy
20 hours ago • updated 53 minutes ago
pickingastar
• 0
0
votes
1
reply
47
views
Subsetting RNAseq data | voomaByGroup()
limma
updated 7 hours ago by
Gordon Smyth
50k • written 20 hours ago by
Anna
• 0
0
votes
2
replies
304
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 19 hours ago by
Michael Love
42k • written 1 day ago by
Ken C
• 0
0
votes
2
replies
104
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 19 hours ago by
Michael Love
42k • written 1 day ago by
shaunpeterson
• 0
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 1 day ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
0
votes
3
replies
96
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 1 day ago by
damian.szk
▴ 80 • written 1 day ago by
ninidea
• 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 1 day ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
2
votes
5
replies
214
views
Error while installing BiocManager::install("org.Vdahliae.eg.db")
org.vdahlaie.eg.db
Bioconductor
3 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
240
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
5 days ago • updated 2 days ago
BioinfGuru
▴ 30
0
votes
2
replies
107
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
2 days ago
makala
• 0
2
votes
2
replies
375
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 2 days ago
Matthew Thornton
▴ 360
0
votes
0
replies
49
views
determine k during RUVSeq
RUVSeq
RUVnormalize
2 days ago
Ειρήνη
• 0
4
votes
9
replies
249
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 2 days ago by
ATpoint
★ 4.1k • written 4 days ago by
pangtaihin
• 0
2
votes
3
replies
99
views
Problem installing ChAMP on a MacBook
ChAMP
updated 2 days ago by
shepherl
3.9k • written 3 days ago by
Galia
• 0
0
votes
0
replies
49
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
2 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
2 days ago
oliverelijhan
0
0
votes
0
replies
66
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
43
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
38
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
3 days ago
k200987
• 0
2
votes
3
replies
121
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
Guillermo
• 0
0
votes
2
replies
751
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 3 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
4
replies
127
views
error running enricher from clusterprofiler
clusterProfiler
cluster
3 days ago
Yael
• 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 3 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
1
vote
2
replies
125
views
Can log2cpm be used for proteomics data normalization?
metaMSdata
4 days ago • updated 3 days ago
Daniel
• 0
4
votes
5
replies
327
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
13 days ago • updated 3 days ago
Chris
▴ 10
0
votes
2
replies
950
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 3 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
2
votes
1
reply
71
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 3 days ago by
Alejandro Reyes
★ 1.9k • written 5 days ago by
Sara
• 0
0
votes
3
replies
111
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 3 days ago by
Michael Love
42k • written 4 days ago by
Kasper
• 0
1
vote
2
replies
93
views
Erroe when using makeOrgPackageFromNCBI()
AnnotationForge
4 days ago • updated 3 days ago
Patadù
▴ 10
0
votes
0
replies
37
views
Difference in Contrast in DiffBind
DiffBind
3 days ago
zzrammal
• 0
1
vote
2
replies
204
views
Citation for edgeR user guide
edgeR
written 25 days ago by
k___
▴ 30
1
vote
3
replies
244
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
0
votes
8
replies
498
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 5 days ago by
Eric Katagirya
• 0
0
votes
2
replies
128
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 4 days ago by
zhouwanding
▴ 10 • written 6 days ago by
Seungmin
• 0
1
vote
0
replies
327
views
News:
Last Call: Nominations for Bioconductor Awards 2024! Deadline May 15
Recognition
Awards
Bioconductor
Bioc204
8 weeks ago • updated 4 days ago
shepherl
3.9k
0
votes
2
replies
101
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
0
votes
1
reply
91
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 4 days ago by
Michael Love
42k • written 5 days ago by
piemmea
• 0
0
votes
44
replies
3.1k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 4 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
1
vote
0
replies
58
views
News:
Ensembl 112 has been released.
ensembldb
biomaRt
ensemblrelease
4 days ago
Aleena
▴ 30
0
votes
3
replies
175
views
ChAMP installation issue
Cha
ChAMP
6 days ago • updated 5 days ago
e1271094
• 0
0
votes
0
replies
52
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
5 days ago
Researcher
• 0
3
votes
4
replies
280
views
Store output of matchPWM()
biostrings
Biostrings
17 days ago • updated 5 days ago
mat149
▴ 70
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 5 days ago by
bandconductor
• 0 • written 3.6 years ago by
ZheFrench
▴ 60
0
votes
1
reply
136
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 6 days ago by
Guido Hooiveld
★ 4.0k • written 6 days ago by
aogunbaw
• 0
2
votes
2
replies
276
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 days ago • updated 6 days ago
zzrammal
• 0
49 results • Page
1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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