0
votes
1
reply
1.2k
views
two questions about limma
Microarray limma Microarray limma
updated 19 hours ago by 53k • written 18.8 years ago by ▴ 240
0
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1
reply
26
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Question about DESeq2 Design for Paired Treatment Study
DESeq2
updated 2 hours ago by ★ 5.0k • written 1 day ago by • 0
0
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1
reply
50
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problem reading bam files into nucleR
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2 days ago • updated 14 hours ago efoss ▴ 10
0
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0
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24
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News: EuroBioC2026 abstract submission is open!
Conference Bioconductor
3 days ago laurah ondari • 0
0
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0
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42
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PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
4 days ago bolusharris • 0
0
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0
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36
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DECIPHER DesignProbes unable to design FISH-probes
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5 days ago vreinmuth • 0
0
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1
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1.1k
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p.adjust BH Question
updated 5 days ago by 53k • written 14.2 years ago by ▴ 10
1
vote
4
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222
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Large logFC but somewhat high FDR
limpa
6 days ago • updated 5 days ago JKim • 0
0
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0
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56
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Job: Bioinformatician at the Lausanne University Hospital
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5 days ago story.benjamin ▴ 20
3
votes
5
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273
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upstream git branches of bioc-release
Bioconductor
written 6 days ago by ▴ 10
0
votes
2
replies
108
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limpa - drivers for unusually high standard error?
limpa
updated 6 days ago by 53k • written 6 days ago by • 0
1
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3
replies
1.8k
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How can I correctly use phyloseq with Docker?
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updated 8 days ago by ★ 4.0k • written 7 months ago by • 0
0
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1
reply
360
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Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace FlowCytometry
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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1.0k
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Install old version of DESeq2
apeglm Install DESeq2 version
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
votes
1
reply
322
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Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO Bioconductor Arabidopsis_thaliana_Data
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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311
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ORFik: spliced 5utr regions
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updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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354
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BiocManager::install() doesn't work
Install Biocond
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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1
reply
279
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Results with PON give more variants
mutect2 variants pon
updated 8 days ago by ★ 4.0k • written 4 months ago by ▴ 10
0
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1
reply
226
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Empty boxes in treemap plot rrvgo package
rrvgo
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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1
reply
230
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CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek CRISPR
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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2
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400
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Feedback needed on new user-friendly BED file tool
bedbaser offtopic
updated 8 days ago by ★ 4.0k • written 4 months ago by • 0
0
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1
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204
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sigDF object in sesame
sesame sesameData
updated 8 days ago by ★ 4.0k • written 3 months ago by • 0
0
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3
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320
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Create consensusMatrix for codon bases
Biostrings
updated 8 days ago by ★ 4.0k • written 3 months ago by • 0
0
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2
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396
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Memory error while running alignments
DECIPHER Alignment
updated 8 days ago by ★ 4.0k • written 3 months ago by • 0
1
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11
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1.3k
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 8 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
224
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Finding duplicated entries in GRangesList
GenomicRanges
updated 9 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
218
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DESeq2 on non-RNASeq counts data
DESeq2
updated 9 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
2
replies
384
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After running samtools, the featureCounts command crashed.
RNASeqData Bioconductor RNASeq
updated 5 days ago by • 0 • written 10 weeks ago by • 0
0
votes
1
reply
475
views
Problem with the TMB plot
Bioconductor
updated 9 days ago by ★ 4.0k • written 10 weeks ago by • 0
3
votes
5
replies
359
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
10 days ago • updated 5 days ago Ahmed Salah • 0
0
votes
1
reply
244
views
mzR-Rcpp compiler version issue
Rcpp Perseus mzR
updated 11 days ago by 1.6k • written 3 months ago by • 0
2
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3
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462
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DESeq2 design for haplotype MPRA
Bioconductor
updated 10 days ago by • 0 • written 6 weeks ago by • 0
0
votes
1
reply
186
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Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 11 days ago by ★ 4.0k • written 19 days ago by • 0
0
votes
0
replies
206
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Corrupted SQLite while trying to install PANTHER.db?
SQLite PANTHER.db
updated 11 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
0
replies
273
views
org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
MAMDC4 org.Ss.eg.db AnnotationDbi
updated 11 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
269
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 11 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
reply
289
views
Extract snp information from genomic regions with biomaRt -> "oaries_snp"
biomaRt
updated 11 days ago by ★ 4.0k • written 12 weeks ago by • 0
0
votes
2
replies
285
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3-factor DESeq2 trime-series analysis
time-series DESeq2
updated 11 days ago by ★ 4.0k • written 11 weeks ago by • 0
0
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1
reply
247
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Questions about pseudo counts from RUVSeq
RUVSeq
updated 11 days ago by ★ 4.0k • written 11 weeks ago by • 0
0
votes
0
replies
243
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Problem with viewGO(ref_path) in SpliceWiz
Bioconductor SpliceWiz
updated 11 days ago by ★ 4.0k • written 10 weeks ago by • 0
0
votes
0
replies
243
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GOseq Probability Weight Function bad fit
goseq
updated 11 days ago by ★ 4.0k • written 9 weeks ago by • 0
0
votes
0
replies
92
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[DESeq2] Changing dispersion estimates between runs of DESeq2
DESeq2
updated 11 days ago by ★ 4.0k • written 17 days ago by • 0
0
votes
2
replies
109
views
APAlyzer
APAlyzer
updated 11 days ago by ★ 4.0k • written 13 days ago by ▴ 10
2
votes
2
replies
232
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
12 days ago • updated 11 days ago jamie.gearing ▴ 60
0
votes
2
replies
158
views
Alternative to BrainArray custom CDF packages for Affymetrix chips?
Bioconductor
updated 11 days ago by ★ 4.1k • written 15 days ago by ▴ 600
1
vote
2
replies
197
views
Error installing Seqinfo
Seqinfo S4Vectors
updated 13 days ago by 4.2k • written 15 days ago by • 0
1
vote
0
replies
58
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News: Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Bioconductor
16 days ago Maria Doyle ▴ 110
0
votes
4
replies
181
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
16 days ago • updated 13 days ago Denise • 0
2
votes
2
replies
164
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Post translational modifications and phosphoproteomics in limpa?
limpa
17 days ago • updated 10 days ago james.eapen • 0
0
votes
1
reply
110
views
Add additional maintainer for MOFA2
MOFA2
updated 20 days ago by 4.2k • written 20 days ago by • 0
46,683 results • Page 1 of 934
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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