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Is it still possible to do batch correction for my data?
RNASeq
edgeR
5 days ago • updated 4 hours ago
LBJ0744
• 0
0
votes
0
replies
59
views
News:
The BioC2026 Call for Abstracts deadline has been extended
Bioconductor
BioC2026
Conference
3 days ago
laurah ondari
• 0
0
votes
1
reply
116
views
specifying refColumn in calcNormFactors()
edgeR
limma
updated 3 days ago by
Gordon Smyth
53k • written 5 days ago by
Nova
• 0
0
votes
1
reply
104
views
Sex prediction in sesame for EPICV2
sesame
EPICv2manifest
updated 4 days ago by
Tim Peters
▴ 230 • written 4 days ago by
poojitha.stemcell
▴ 10
0
votes
0
replies
61
views
APAlyzer gives zero/NaN matrix?
APAlyzer
4 days ago
lynn.hua.lee
• 0
0
votes
4
replies
210
views
Convergence Issues and Model Selection DESeq2
DESeq2
6 days ago • updated 4 days ago
dani.guan.3
• 0
5
votes
3
replies
947
views
Limma-voom sample weights and impact on DEG numbers
limma
written 11 weeks ago by
A.Barden
▴ 20
2
votes
2
replies
196
views
Quick two questions on limpa
limpa
updated 2 days ago by
Gordon Smyth
53k • written 6 days ago by
J Kim
• 0
0
votes
2
replies
143
views
recursively counting package dependencies
BiocPkgTools
7 days ago • updated 6 days ago
Helena
• 0
0
votes
2
replies
207
views
Subsetting DDS object for individual conditions over time
DESeq2
11 days ago • updated 10 days ago
A
▴ 60
2
votes
2
replies
202
views
tximeta cannot open annotation gtf?
tximeta
Bioconductor
updated 12 days ago by
Michael Love
43k • written 13 days ago by
lynn.hua.lee
• 0
1
vote
2
replies
230
views
GSEA error
gsea
GSEABenchmarkeR
13 days ago • updated 11 days ago
Adithi
• 0
0
votes
0
replies
19
views
Spam:
TOGAF Certification Training in Dallas TX | Enterprise Architecture & ADM Mastery
mouse430a2.db
BSgenome.Hsapiens.UCSC.hg17.masked
13 days ago
zebaafarheensprintzeal
0
0
votes
3
replies
198
views
Unable to find ENTREZ IDs
entrezid
ensembldb
14 days ago • updated 13 days ago
Adithi
• 0
0
votes
0
replies
14
views
Spam:
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TxDb.Dmelanogaster.UCSC.dm3.ensGene
DiseaseModel
14 days ago
Clarasmith
0
0
votes
1
reply
266
views
bcftools norm Equivalent
Rsamtools
written 6 weeks ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
377
views
Inconsistencies between accessor functions for TxDb databases with selected seqlevels.
TxDb
GenomicFeatures
GenomeInfoDb
written 4 weeks ago by
dbsgtk
• 0
0
votes
0
replies
14
views
Spam:
CBD Cream Boxes by BoxesGen & Custom Boxes Lab
mouse430a2.db
Cepo
19 days ago
hiraboxesgen
0
3
votes
4
replies
781
views
Issue loading and downloading Bioconductor 3.22 packages after update
VariantAnnotation
Bioconductor
SNPlocs.Hsapiens.dbSNP155.GRCh38
20 days ago
strawberry3
• 0
0
votes
3
replies
327
views
Reproducibility of code in various Bioconductor versions
VariantAnnotation
SNPlocs.Hsapiens.dbSNP155.GRCh38
dbSNP
GenomicRanges
updated 20 days ago by
Gordon Smyth
53k • written 21 days ago by
strawberry3
• 0
1
vote
3
replies
451
views
Question on processing compound protein groups in limpa
limpa
updated 8 days ago by
brianpeterson1210
• 0 • written 24 days ago by
J Kim
• 0
0
votes
1
reply
184
views
Signature for msVIPER from paired bulk RNAseq data
viper
Normalization
pair
updated 23 days ago by
Michael Love
43k • written 25 days ago by
Kryštof
• 0
3
votes
2
replies
290
views
Correct usage of limpa for protein input
limpa
written 25 days ago by
miro165sabo
• 0
0
votes
0
replies
166
views
News:
Registration for EuroBioC2026 is open!
Bioconductor
Conference
24 days ago
laurah ondari
• 0
5
votes
3
replies
373
views
Which preprocessing steps are needed before running limpa?
Normalization
limpa
updated 25 days ago by
Gordon Smyth
53k • written 4 weeks ago by
miro165sabo
• 0
3
votes
3
replies
352
views
Can sample-level weights be used when analysing GSVA scores in limma?
limma
26 days ago • updated 19 days ago
A.Barden
▴ 20
0
votes
3
replies
323
views
Questions about bacon QC and correction on EWAS results
bacon
written 8 weeks ago by
sup0903
• 0
0
votes
0
replies
14
views
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mouse430a2.db
28 days ago
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0
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0
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15
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Spam:
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mouse430a2.db
28 days ago
cyber
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0
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0
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13
views
Spam:
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28 days ago
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0
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11
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28 days ago
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29 days ago
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4 weeks ago
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0
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4 weeks ago
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25
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rexposome
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Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
limpa
updated 4 weeks ago by
Gordon Smyth
53k • written 4 weeks ago by
miro165sabo
• 0
0
votes
1
reply
118
views
Testing subgroup-specific interactions in DEXSeq
DEXSeq
RNASeqData
Transcriptomics
4 weeks ago • updated 27 days ago
palanikumars2
• 0
0
votes
0
replies
202
views
Job:
Postdoctoral Associate - Bioinformatics Education - Baylor College of Medicine - Houston, Texas, USA
JobPosting
Outreach
Education
Postdoc
Bioinformatics
4 weeks ago
Erik Wright
▴ 160
1
vote
3
replies
553
views
Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy names?
silva
decipher
DECIPHER
updated 27 days ago by
Erik Wright
▴ 160 • written 4 weeks ago by
Korneel
• 0
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Comment: Is it still possible to do batch correction for my data?
by
LBJ0744
• 0
Thank you so much! I will check out this method.
Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label
by
nytwordlehints
• 0
Amazing insights! I learned a lot from this.[pokemon overlord][1] [1]: https://pokemonoverlord.com
Answer: Is it still possible to do batch correction for my data?
by
Gordon Smyth
53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors()
by
Gordon Smyth
53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2
by
Tim Peters
▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
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Answer: Is it still possible to do batch correction for my data?
Answer: Is it still possible to do batch correction for my data?
A: Fundamental questions about DESeq2 and RUVs in targeted gene set of 500
Answer: p-adjusted values in multiple comparisons
Comment: p-adjusted values in multiple comparisons
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