2
votes
6
replies
1.6k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
21 months ago Lily Cheang ▴ 10
3
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8
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1.4k
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Constrast for Time Course Experiments using Limma
limma
21 months ago dl17032000 • 0
1
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4
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932
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DESeq2 Replicates
DESeq2 RNASeq
21 months ago kcarey • 0
2
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6
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1.0k
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Factor vs Character in design
DESeq2
21 months ago James Aiden • 0
1
vote
3
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1.1k
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
21 months ago I-Hsuan Lin ▴ 10
4
votes
7
replies
1.9k
views
weird volcano plot
DESeq2
updated 21 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
1
reply
751
views
DEseq2 dispersion plot
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updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
0
replies
706
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News: Nominations for Bioconductor Awards 2024!
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22 months ago • updated 21 months ago shepherl 4.2k
0
votes
2
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1.1k
views
News: BioC2024 abstract submission is open!
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0
votes
0
replies
624
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TCGAbiolinks STAD project 450k Methylation Beta Value data
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21 months ago Giovanni Calice ▴ 160
0
votes
0
replies
1.1k
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Proteomics JobPosting SingleCell Spatial SpatialExperiment
21 months ago Peter Hickey ▴ 760
1
vote
3
replies
2.2k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
21 months ago • updated 15 months ago s.malik • 0
0
votes
0
replies
1.0k
views
Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
0
replies
690
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21 months ago info ▴ 10
1
vote
1
reply
1.2k
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 21 months ago by ★ 3.6k • written 22 months ago by • 0
0
votes
1
reply
571
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
3
replies
1.1k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 10
0
votes
11
replies
1.9k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 21 months ago by 53k • written 22 months ago by • 0
0
votes
2
replies
1.1k
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Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
8
votes
6
replies
1.3k
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DGE analysis with LIMMA
limma
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
0
replies
789
views
News: BioC2024 registration is now open!
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21 months ago Maria Doyle ▴ 110
0
votes
1
reply
897
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error in Matrix function
MatrixQCvis
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
3
replies
959
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Would I treat surrogate variables as batches?
DESeq2 sva
updated 21 months ago by 68k • written 21 months ago by ▴ 10
1
vote
0
replies
773
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag SplicedAlignment SGSeq minimap2
21 months ago jk ▴ 10
0
votes
0
replies
596
views
Can I combine collinear variables into a single value
BatchEffect limma
21 months ago Harrsha • 0
0
votes
1
reply
709
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 21 months ago by 68k • written 21 months ago by • 0
6
votes
5
replies
2.3k
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC minifi
written 21 months ago by • 0
1
vote
4
replies
1.0k
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
21 months ago hmillike • 0
0
votes
0
replies
1.1k
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
21 months ago vipul14 • 0
0
votes
0
replies
639
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R ATACseqQC
21 months ago danalvoronov ▴ 10
2
votes
1
reply
1.2k
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
1
reply
720
views
ExactTest vs QLFTest
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
2
replies
777
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arm64 Update to flowWorkspace (4.14.2)
flowWorkspace
21 months ago rgong1 • 0
0
votes
0
replies
519
views
lfcSE
RGSEA
21 months ago Gordon • 0
0
votes
1
reply
685
views
Matrix multiplication error to estimate telomere length
methylclockData minfi methylclock minfidata
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
3
replies
926
views
impute.knn produces different results based on matrix order
impute
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
1
reply
486
views
few significant genes from DESeq2 analysis
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
3
replies
1.2k
views
Differential enrichment analysis
limma Differentialenrichmentanalysis DEP
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
2
replies
1.8k
views
Impute does not work
impute
22 months ago • updated 21 months ago Laura • 0
2
votes
3
replies
1.1k
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
21 months ago jbgnielson • 0
0
votes
4
replies
1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
21 months ago mperalc • 0
0
votes
2
replies
1.2k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 22 months ago by 53k • written 22 months ago by • 0
1
vote
7
replies
1.8k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 14 months ago by • 0 • written 22 months ago by • 0
0
votes
0
replies
628
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
22 months ago thomas.heigl.ibk • 0
0
votes
1
reply
1.9k
views
error in mapIds function
mapIds biomaRt
updated 22 months ago by 700 • written 22 months ago by • 0
1
vote
4
replies
1.5k
views
DEseq2 coefficient
DESeq2 coefficient
22 months ago • updated 19 months ago JKim • 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 22 months ago by ▴ 10
2
votes
1
reply
760
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
0
votes
1
reply
768
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
2
votes
2
replies
846
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
22 months ago Hope ▴ 10
46,696 results • Page 30 of 934
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Replies
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 …
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Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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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…
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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