0
votes
3
replies
1.4k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.3 years ago by ★ 1.9k • written 2.3 years ago by • 0
0
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3
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2.2k
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Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
861
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
1
vote
6
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1.7k
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Limma dispersed distribution of log fold change
limma
written 2.3 years ago by • 0
1
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4
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1.7k
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How to find differentially expressed proteins from multiple conditions (>2) using proDA?
Proteomics proDA MultipleComparison
2.3 years ago t.b.n.nguyen-9 • 0
0
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1
reply
1.3k
views
How to properly compare the group-specific samples using DEseq2
DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
0
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14
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4.6k
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Error while preprocessing raw data from methylation array using minfi package
minfi
updated 22 months ago by • 0 • written 2.3 years ago by • 0
0
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0
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NAs in tabular output from DNAcopy
Bioconductor DNAcopy
2.3 years ago NewtoBioconductor • 0
5
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13
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4.4k
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Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
976
views
Sample size estimation for RNAseq experiment with more than 2 conditions
SSPA ssizeRNA RnaSeqSampleSize
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
1
reply
837
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
2
votes
4
replies
2.1k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 10
0
votes
5
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1.6k
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How to use contrast with multiple treatments?
RNASeqdataanalysis DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
1
vote
0
replies
876
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Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
2.3 years ago svlachavas ▴ 840
0
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0
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2.1k
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Tutorial: Read data file containing both counts and annotation into edgeR
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2.3 years ago Gordon Smyth 53k
1
vote
2
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1.5k
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Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 5 months ago by • 0 • written 2.3 years ago by ▴ 10
0
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1
reply
1.3k
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Error retrieving cytobands from UCSC
biovizBase biovi
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 150
0
votes
2
replies
3.5k
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apply clusterProfiler::simplify on merge_result list
clusterProfiler
2.3 years ago Valéria • 0
0
votes
1
reply
1.1k
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
1.1k
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
2.3 years ago Mark ▴ 10
2
votes
2
replies
1.7k
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DESeq2 results - Annotating and exporting results
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
votes
7
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1.7k
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DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
2.3 years ago casco ▴ 10
2
votes
7
replies
5.3k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.3 years ago by • 0 • written 4.7 years ago by ▴ 20
1
vote
2
replies
1.3k
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DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
2.4 years ago • updated 2.3 years ago Junsik • 0
1
vote
0
replies
1.1k
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Job: EMBL-EBI Data resources: Functional Genomics and Single Cell Biology Team Leader
JobPosting
2.3 years ago Wolfgang Huber ★ 13k
1
vote
4
replies
966
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BioNero - problem with module_trait_cor function
BioNERO
2.3 years ago matevz.likar • 0
0
votes
1
reply
1.0k
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SVA for MatrixeQTL - which "variable of interest"?
matrixeqtl sva
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
9
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1.8k
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DESeq2: How to estimate effects of one factor controlling for other factors?
DESeq2
2.3 years ago mjd275 • 0
1
vote
8
replies
4.3k
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Significantly regulated genes produced by only a few affected samples
deseq2
written 7.8 years ago by ▴ 60
0
votes
9
replies
2.0k
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How long does it usually take to complete dream() from start to finish?
variancePartition mixedmodel dream
2.3 years ago hayleyw • 0
3
votes
4
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4.1k
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Protein differential Expression analysis
differential expression proteomics
updated 2.3 years ago by ★ 5.0k • written 8.0 years ago by • 0
2
votes
14
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
2
votes
12
replies
2.9k
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P-value inflation?
DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
1
vote
3
replies
1.3k
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
2
replies
924
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DiffBind error
DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
votes
0
replies
846
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Getting CDS 5'/CDS3' incomplete flags info from ENSEMBL using biomaRt
biomaRt
2.3 years ago ali.oghabian • 0
1
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2
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1.4k
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DESeq2 batch design
DESeq2
updated 2.3 years ago by ★ 1.4k • written 2.4 years ago by ▴ 10
2
votes
2
replies
990
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Broken UNITE 9.0 link (General FASTA Release)
dada2 UNITE
2.3 years ago GlycineMax • 0
1
vote
4
replies
1.3k
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running Bioconductor Docker images only works with versions <= 3.15
Bioconductor
2.3 years ago patrick.turko • 0
0
votes
1
reply
858
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TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
864
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Package "Netboost" is an Unix-only package, how can I install it in R?
Bioconductor netboost
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
0
replies
918
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome ?
Metagenomics metagenomeSeq microbiome phyloseq microbiomeDataSets
2.3 years ago Mohamed ▴ 30
0
votes
8
replies
3.6k
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Question about filterByExpr function edgeR
edgeR
2.3 years ago lucap • 0
0
votes
1
reply
1.1k
views
Getting NAs in both p-values (normal and adjusted) in DEseq2
DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
892
views
Cant post a bug report
msa
updated 23 months ago by ▴ 50 • written 2.3 years ago by • 0
0
votes
3
replies
1.2k
views
Is it possible to extract the expression of a single group without making comparisons?
MicroarrayData hta20transcriptcluster.db
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
0
votes
2
replies
902
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 2.3 years ago by • 0
8
votes
15
replies
3.3k
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PCA percent variance DESeq2
PCA DESeq2
2.3 years ago IUH • 0
1
vote
6
replies
3.5k
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
7
replies
2.8k
views
error with champ.load
ChAMP champ methylation
updated 2.3 years ago by • 0 • written 5.7 years ago by • 0
46,696 results • Page 44 of 934
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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