8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by ▴ 30
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 8 months ago by 50k • written 22 months ago by ▴ 30
5
votes
7
replies
488
views
DEG Filtering
MicroarrayData limma Genefiltering
updated 7 weeks ago by 50k • written 9 weeks ago by • 0
4
votes
7
replies
901
views
weird volcano plot
DESeq2
updated 10 weeks ago by • 0 • written 6 months ago by ▴ 10
3
votes
7
replies
884
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
2
votes
7
replies
2.0k
views
How to generate custom annotation for rat genome rn6 in ChIPQC
ChIPQC annotation rn6
updated 4 months ago by • 0 • written 3.7 years ago by • 0
1
vote
7
replies
878
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
1
vote
7
replies
6.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 11 weeks ago by 16k • written 6 months ago by ▴ 10
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
6
votes
7
replies
972
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 7 months ago by ▴ 20
0
votes
7
replies
689
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC ATACSeq
updated 11 weeks ago by ▴ 10 • written 5 months ago by • 0
4
votes
7
replies
1.1k
views
Fishpond/Swish Interaction Test Error
fishpond swish
11 months ago Miguel ▴ 20
0
votes
7
replies
440
views
Internet connection for Bioconductor packages in Rstudio in Iran...
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7 weeks ago • updated 6 weeks ago needNGS • 0
6
votes
7
replies
608
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
7
replies
3.0k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
0
votes
7
replies
449
views
DESeq filtering specific to contrasts
DESeq2
updated 29 days ago by 42k • written 3 months ago by • 0
1
vote
7
replies
1.7k
views
enrichGOgradient color change
clusterProfiler
updated 8 weeks ago by ★ 4.0k • written 6 months ago by • 0
0
votes
7
replies
459
views
DESeq2 filtering vs edgeR filtering
DESeq2
9 weeks ago • updated 7 weeks ago fr8712ca-s • 0
0
votes
7
replies
749
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 25 days ago shepherl 3.9k
1
vote
7
replies
1.3k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
2
votes
7
replies
642
views
How do you post on this forum?
pcaMethods
3 months ago yousavdj • 0
0
votes
7
replies
1.7k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
2
votes
7
replies
383
views
deseq2 results
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11 days ago • updated 7 days ago sajadahmad41454 • 0
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 7 months ago by ▴ 10 • written 6.6 years ago by ▴ 30
3
votes
7
replies
1.9k
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Installing densvis on a Singularity container
densvis docker
updated 11 months ago by ▴ 160 • written 12 months ago by 65k
2
votes
7
replies
2.5k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
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updated 7 months ago by • 0 • written 3.4 years ago by ▴ 20
0
votes
7
replies
1.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
13 months ago • updated 11 months ago Ti • 0
1
vote
7
replies
359
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
23 days ago • updated 22 days ago pl23 • 0
0
votes
7
replies
690
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
0
votes
7
replies
1.1k
views
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
votes
7
replies
970
views
Errors with running learn.bn function and setting toCompact to TRUE in one.step.pigengene function in Pigengene package
Pigengene
6 months ago kjngo ▴ 40
0
votes
7
replies
495
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
7
replies
892
views
Permutation test in DESeq2?
DESeq2
updated 8 months ago by 42k • written 8 months ago by • 0
3
votes
7
replies
908
views
DESeq2 alternative hypyothesis: testing for genes NOT significantly downregulated
DESeq2
8 months ago casco ▴ 10
1
vote
7
replies
4.6k
views
Problems Installing biomaRt
biomaRt
updated 6 months ago by 65k • written 2.1 years ago by ▴ 20
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by 50k • written 8.0 years ago by • 0
0
votes
7
replies
1.9k
views
error with champ.load
ChAMP champ methylation
updated 9 months ago by • 0 • written 4.1 years ago by • 0
2
votes
7
replies
4.8k
views
Installing Local packages in Bioconductor
package
updated 9 months ago by • 0 • written 2.0 years ago by • 0
0
votes
7
replies
2.7k
views
LIMMA: plotMDS
updated 9 months ago by 50k • written 12.0 years ago by ▴ 180
0
votes
7
replies
1.7k
views
Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install instal
updated 6 months ago by 65k • written 6 months ago by • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
7
replies
5.5k
views
error with champ.load
champ
written 6.5 years ago by ▴ 10
2
votes
7
replies
1.8k
views
Issue with GSVA using dgCMatrix
GSVA
updated 10 weeks ago by ▴ 10 • written 2.9 years ago by • 0
0
votes
7
replies
364
views
Methylation Analysis experiment design using Limma
DNAMethylation limma methylationArrayAnalysis
4 weeks ago • updated 26 days ago hortense96 • 0
4
votes
7
replies
739
views
DESeq2 unable to handle large count values
DESeq2
updated 8 weeks ago by 42k • written 6 months ago by • 0
2
votes
7
replies
538
views
distanceToNearest
rtracklayer ranges distanceToNearest
4 months ago robjohn70000 • 0
6
votes
7
replies
797
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 6 months ago by • 0 • written 4.8 years ago by ▴ 50
1,737 results • Page 4 of 35
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
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…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
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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Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
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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