8
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7
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1.2k
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Why is DMRcate not available for Bioconductor version 3.18?
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How to generate custom annotation for rat genome rn6 in ChIPQC
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updated 4 months ago by • 0 • written 3.7 years ago by • 0
1
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7
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878
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DuplicateCorrelation() block by duplicate sample or by cell line ?
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updated 5 months ago by 50k • written 7 months ago by • 0
4
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7
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738
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5
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7
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different number of DEG because of outliers
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1
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7
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scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
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2
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EdgeR glmLRT vs glmQLFTest
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updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
6
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7
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972
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[Bug] Segfault in edgeR::cpm
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updated 6 months ago by ★ 4.1k • written 7 months ago by ▴ 20
0
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7
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DiffBind - question about showing significant difference on peaks with 0 fold change
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13 months ago • updated 11 months ago Ti • 0
1
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7
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359
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Math expression in shapeCustom legend in EnhancedVolcano
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23 days ago • updated 22 days ago pl23 • 0
0
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7
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updated 5 months ago by ▴ 780 • written 5 months ago by • 0
0
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7
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1.1k
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Cannot open URL for StringDB protein.links.v11.5/9606.protein.links.v11.5.txt.gz
STRINGdb
updated 9 months ago by ▴ 80 • written 9 months ago by • 0
2
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7
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969
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Errors with running learn.bn function and setting toCompact to TRUE in one.step.pigengene function in Pigengene package
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6 months ago kjngo ▴ 40
0
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7
replies
495
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error in reading idat files and creating rgset
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updated 3 months ago by 65k • written 3 months ago by • 0
1
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7
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892
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Permutation test in DESeq2?
DESeq2
updated 8 months ago by 42k • written 8 months ago by • 0
3
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7
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908
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DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
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8 months ago casco ▴ 10
1
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7
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Problems Installing biomaRt
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updated 6 months ago by 65k • written 2.1 years ago by ▴ 20
2
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Installing Local packages in Bioconductor
package
updated 9 months ago by • 0 • written 2.0 years ago by • 0
6
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Adding a group of samples reduces DEGs in other groups
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updated 9 months ago by 50k • written 9 months ago by ▴ 10
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LIMMA: plotMDS
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updated 6 months ago by 65k • written 6 months ago by • 0
5
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7
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Question about setting threshold using filtering by expression on genes in edgeR
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updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
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error with champ.load
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2
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updated 10 weeks ago by ▴ 10 • written 2.9 years ago by • 0
0
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distanceToNearest
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4 months ago robjohn70000 • 0
4
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7
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should statmod be a dependency of limma and not a suggests?
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updated 9 months ago by 50k • written 8.0 years ago by • 0
0
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7
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error with champ.load
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updated 9 months ago by • 0 • written 4.1 years ago by • 0
8
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7
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
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updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
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7
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Single Sample GSEA (ssGSEA) and dynamic range of expression
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updated 5 months ago by ▴ 10 • written 6.8 years ago by ▴ 130
1
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7
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Error using champ.import
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updated 4 weeks ago by • 0 • written 10 months ago by • 0
5
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threshold to filter lowly expressed genes
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updated 4 months ago by • 0 • written 7.2 years ago by • 0
0
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7
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689
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ATACseqQC shiftGAlignmentsList() problem
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Fishpond/Swish Interaction Test Error
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11 months ago Miguel ▴ 20
0
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7
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438
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Internet connection for Bioconductor packages in Rstudio in Iran...
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7 weeks ago • updated 6 weeks ago needNGS • 0
6
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7
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readDGE in edgeR giving me path names as sample names
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updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
7
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3.0k
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Technical details of DiffBind correlation analysis
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updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
0
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7
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449
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DESeq filtering specific to contrasts
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updated 29 days ago by 42k • written 3 months ago by • 0
4
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7
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Confused about the CPM and TMM normalization in edgeR
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updated 8 months ago by 50k • written 22 months ago by ▴ 30
1
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7
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enrichGOgradient color change
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updated 8 weeks ago by ★ 4.0k • written 6 months ago by • 0
0
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7
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DESeq2 filtering vs edgeR filtering
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9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
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11 weeks ago • updated 25 days ago shepherl 3.9k
1
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7
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Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
2
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7
replies
642
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How do you post on this forum?
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3 months ago yousavdj • 0
0
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7
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Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
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updated 6 months ago by 65k • written 6 months ago by • 0
2
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7
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382
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deseq2 results
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Effect of lfcThreshold on p-value in DESeq2
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updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
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updated 11 months ago by ▴ 160 • written 12 months ago by 65k
2
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Blood cell composition adjustment in methylation EPIC array: ChAMP
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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…
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Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
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Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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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?
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