0
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8
replies
2.0k
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DESeq2 cannot relevel
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4.2 years ago Jorge • 0
0
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1
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1.1k
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Error in flowCore::read.FCS(): Error in uint2double(splitted, endian == "big") : vector
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4.2 years ago Rainer • 0
3
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2
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5.2k
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gseGO input list
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0
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0
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1.5k
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Job: Postdoctoral Scientist in Statistical Bioinformatics, WEHI, Melbourne, Australia
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Multiple testing correction for p.scores in FELLA
FELLA
4.2 years ago sergi.picart ▴ 20
0
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3
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1.7k
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ENSEMBL BIOMART INTERFACE DOWN?
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updated 4.2 years ago by ★ 6.6k • written 4.2 years ago by • 0
2
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5
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DESeq2: error while ploting figure
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updated 4.2 years ago by 43k • written 4.2 years ago by • 0
5
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3
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DeSeq2 Comparing One group vs Two groups
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written 4.2 years ago by ▴ 10
8
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News: Bioconductor 3.14 is Released!
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4.2 years ago shepherl 4.3k
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3
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1.5k
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CAGEr: Problem when running getCTSS
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updated 4.2 years ago by ▴ 180 • written 4.4 years ago by • 0
0
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1
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1.2k
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Import and Analyze 4 GSE12050_GSM304448.gpr microarrays files
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updated 4.2 years ago by 53k • written 4.2 years ago by • 0
1
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12
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4.6k
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Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
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updated 24 months ago by • 0 • written 4.2 years ago by ▴ 380
1
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4
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1.5k
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Advice to use block factor and duplicatecorrelation in RNA-seq experiment
limma
4.2 years ago jfertaj ▴ 30
1
vote
8
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5.5k
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Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
4.2 years ago v.merino.nicolas ▴ 10
0
votes
1
reply
1.4k
views
Same error that DMRcate Error in if (nsig == 0) { : missing value where TRUE/FALSE needed
DMRcate
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 30
0
votes
2
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1.4k
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Error in TFBSTools at SitesetList
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4.2 years ago HELEN • 0
6
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6
replies
2.4k
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Batch effect from to sequencing data at differents depths
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4.2 years ago ary.lech ▴ 10
0
votes
3
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2.4k
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Bioconductor 3.13 installer reports that affyQCReport is not available
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updated 4.2 years ago by ▴ 10 • written 4.3 years ago by • 0
2
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1
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3.8k
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Specify hg19 in using biomaRt getBM function
biomaRt biom
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
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0
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1.3k
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Editing KEGG pathways in R
KEGG
4.2 years ago Jordan • 0
2
votes
4
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4.8k
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How to simply change chromosome names of a GRanges object?
genomicrang GenomicRanges
updated 4.0 years ago by 16k • written 4.2 years ago by ▴ 20
1
vote
1
reply
2.4k
views
DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
0
replies
3.7k
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Circlize - Error: not enough space for cells at track index '5'.
circlize
4.2 years ago lessismore ▴ 20
0
votes
2
replies
1.4k
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problems opening ChAMP
ChAMP
updated 4.2 years ago by ▴ 780 • written 4.2 years ago by • 0
1
vote
3
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1.3k
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Example from TissueEnrich documentation throws error
TissueEnrich
4.2 years ago sarvesh.nikumbh ▴ 10
1
vote
1
reply
2.2k
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Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
votes
0
replies
728
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Error in infinityFlow
infinityFlow
4.2 years ago Niv • 0
0
votes
3
replies
1.9k
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Problem select / ensembl package
ensembldb
4.2 years ago yinnahm • 0
0
votes
2
replies
2.4k
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AnnotationDbi
AnnotationDbi
4.2 years ago Bogdan ▴ 670
1
vote
2
replies
2.1k
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Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks cnv
4.2 years ago raf4 ▴ 30
2
votes
4
replies
2.1k
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DESeq2/edgeR/limma help with most appropriate design matrix
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updated 4.2 years ago by 53k • written 4.3 years ago by • 0
2
votes
1
reply
1.3k
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preprocessReads: Can't remove more than 17 nucleotides
QuasR preprocessReads
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
1
reply
1.1k
views
lfcshrink() and 2 conditions, 3 genotypes
lfcshrink DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
1
reply
680
views
Interaction model genes don't intersect
DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
0
replies
1.6k
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4.2 years ago chao.xing • 0
3
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3
replies
1.1k
views
Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 20
2
votes
2
replies
2.1k
views
[recount3] Merge gene counts tables from multiple projects (SRP)
recount3 recountWorkflow
updated 4.2 years ago by ★ 1.1k • written 4.3 years ago by ▴ 510
0
votes
1
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1.4k
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Different read support for splice junctions using snapcount and recount3
recount3 snapcount
updated 4.2 years ago by ★ 1.1k • written 4.3 years ago by ▴ 20
3
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2
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1.6k
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DESeq2 normalization when using with derfinder
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4.2 years ago Debayan ▴ 20
0
votes
2
replies
1.9k
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Correct workflow for analyzing differentially expressed genes and correlation analyses on TCGA data?
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4.2 years ago mario.keller.1988 ▴ 20
4
votes
1
reply
3.2k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
1
vote
4
replies
1.4k
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Error in designing DESeq2 time pointed experiments
LTR DESeq2
4.2 years ago AZ ▴ 20
0
votes
0
replies
916
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Calculate AUC from CellTiter-Glo luminance data in R
highthroughputassays drc
4.2 years ago yura.grabovska ▴ 30
0
votes
2
replies
1.3k
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results() function and finding the difference of differences
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4.2 years ago Nayrouz • 0
1
vote
0
replies
1.1k
views
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JobPosting
4.2 years ago Laurent Gatto 1.6k
0
votes
1
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818
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pd.ragene.2.0
pd.ragene.2.0.st
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
8
replies
3.7k
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TCL/TK in R
TCL/TK
4.2 years ago Bogdan ▴ 670
1
vote
0
replies
2.2k
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GSEA using clusterProfiler with non-model organism.
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4.2 years ago makrez ▴ 10
3
votes
3
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2.7k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
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4.2 years ago enricoferrero ▴ 680
0
votes
0
replies
897
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Y axis Data Track GVIZ
GVIZ
4.2 years ago • updated 4.1 years ago rbenel ▴ 50
46,726 results • Page 109 of 935
Recent ...
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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