5
votes
7
replies
4.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind pca
updated 4.4 years ago by ★ 5.2k • written 10.2 years ago by ▴ 20
0
votes
1
reply
1.5k
views
accounting for gene length with SeqGSEA
goseq SeqGSEA goseq SeqGSEA
updated 10.2 years ago by • 0 • written 12.6 years ago by ▴ 110
0
votes
2
replies
2.5k
views
Problems installing ChipPeakAnno with newest version of R and Bioconductor
chippeakanno installation
10.2 years ago rebecca.halbach • 0
0
votes
2
replies
2.6k
views
BSGenome::getSeq gives error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome getseq
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
1
vote
1
reply
1.1k
views
Error with DNAStringSet
biostrings iranges
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
2
votes
10
replies
7.0k
views
Install older specific version from an R package that is on the Bioconductor Repository
Bioconductor biocLite R packages oldversion
10.2 years ago svlachavas ▴ 840
13
votes
2
replies
5.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 10.2 years ago by ★ 3.4k • written 10.2 years ago by ▴ 40
4
votes
2
replies
6.5k
views
how can I install packages in docker/R/bioconductor so that they persist?
docker
10.2 years ago anton.kratz ▴ 60
0
votes
3
replies
1.4k
views
Gene Interaction Computation
microarray gene interaction GRN
updated 10.2 years ago by ★ 3.4k • written 10.2 years ago by • 0
25
votes
11
replies
9.3k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq deseq2 edgeR normalization
updated 10.2 years ago by ★ 3.8k • written 10.2 years ago by ▴ 90
0
votes
1
reply
1.7k
views
Is the hgu133plus2.db annotation package outdated ?
hgu133plus2.db
10.2 years ago matheus.cburger ▴ 20
1
vote
1
reply
3.5k
views
[Windows 10] 64. Problem installing biocLite due Warning on non writable directory
installation windows10 not-writable warning message library
10.2 years ago juancaf • 0
2
votes
2
replies
3.0k
views
DMRcate cpg.annotate error
dmrcate design matrix
updated 10.2 years ago by ▴ 230 • written 10.2 years ago by ▴ 160
4
votes
7
replies
2.9k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 20
1
vote
1
reply
2.9k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 10
1
vote
3
replies
3.1k
views
Adjust column labels in Heatmap.3
heatmap.3 GMD
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 120
2
votes
5
replies
3.7k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by ▴ 30
1
vote
2
replies
2.2k
views
scanBam with ScanBamParam argument which specified ignores yieldSize. Intentionally?
scanbam scanbamparam rsamtools
updated 10.2 years ago by 25k • written 10.2 years ago by ★ 2.1k
3
votes
2
replies
2.0k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
votes
8
replies
3.0k
views
unable to read FCS: expecting the bitwidth to be the same for all parameters
flowcore read.fcs
10.4 years ago • updated 10.2 years ago michael.gaspar • 0
6
votes
14
replies
4.1k
views
limma with continous covariate depending on gene, 2 block variables, pairing and technical replicates
limma covariate block paired samples technical replicates
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 70
0
votes
5
replies
2.1k
views
Change DiffBind correlation matrix scale
diffbind scale correlation matrix
10.2 years ago eli7javasky • 0
0
votes
1
reply
1.8k
views
RnBeads - test statistics for rnb.run.differential
RnBeads
updated 10.2 years ago by • 0 • written 10.2 years ago by ▴ 120
0
votes
1
reply
1.6k
views
RnBeads and technical replicates in differential analysis
rnbeads replicates
updated 10.2 years ago by • 0 • written 10.2 years ago by ▴ 40
0
votes
4
replies
1.2k
views
New to analysing miccroarrays data
microarray
10.2 years ago kawess • 0
0
votes
2
replies
3.4k
views
Error with , library(limma) !!!
limma
updated 10.2 years ago by ★ 7.9k • written 10.2 years ago by • 0
1
vote
3
replies
3.0k
views
getSequence from biomaRt but Error in martCheck
R biomart ensemble mart
updated 10.2 years ago by 16k • written 10.2 years ago by • 0
1
vote
1
reply
1.3k
views
GRASP2 truncated phenotype descriptions
grasp2 grasp2db annotationhub
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Concatenate individual genomic intervals into populational regions
genomicranges
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 40
0
votes
0
replies
1.3k
views
oposSOM error connecting to ensembl
software error biomart oposSOM
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
0
votes
1
reply
1.6k
views
Error when trying to read cel affymetrix file with custom platform
affymetrix microarrays ae2bioc getAE
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
0
votes
0
replies
1.9k
views
error: no slot of name "expressionFamily" for this object of class "CellDataSet"
monocle bugs
10.2 years ago wanghao1993333 • 0
0
votes
3
replies
2.0k
views
motif scanning using position frequncy matrix of motif in a given set of DNAstringset sequnces?.
motifdb matchpwm motif pwmenrich pwm
10.2 years ago vinod.acear ▴ 50
0
votes
2
replies
1.2k
views
error in reading fcs
flowCore
10.2 years ago yang.chen • 0
2
votes
13
replies
3.5k
views
Error with MEDIPS.createSet in queryHits
medips createset
10.2 years ago Vanilla • 0
0
votes
1
reply
1.4k
views
Diffficulty to use Postgwas package since Biomart web service is down
biomart Problem with biomart's listMarts function
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
1
vote
4
replies
2.1k
views
AGI code in gcrma normalization output
gcrma software error annotation
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 40
0
votes
3
replies
2.2k
views
Error , about QC() !!!
qc
updated 10.2 years ago by 68k • written 10.2 years ago by • 0
4
votes
5
replies
7.3k
views
Unable to use qvalue. Estimated pi0 is <=0
qvalue usage qvalue
updated 10.2 years ago by 53k • written 10.2 years ago by • 0
2
votes
1
reply
5.0k
views
Please suggest any good motif Discovery tool in R-Bioconductor.
motif motifdb meme
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 50
3
votes
5
replies
3.3k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview clusterProfiler KEGGpath visualization Graphviz
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by ▴ 840
0
votes
1
reply
1.7k
views
Annotated heatmap limits
complexheatmap
updated 10.2 years ago by ★ 13k • written 10.2 years ago by • 0
3
votes
2
replies
1.7k
views
getting a list of probe IDs from topTable (limma version 3.18.13)
limma rpy
10.2 years ago rk489 • 0
0
votes
1
reply
2.5k
views
Is there a way to change the name of R package that is already published on bioconductor?
r developers devel
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
3
votes
2
replies
4.4k
views
Limma get all DE genes or filter by logFC
limma microarray rnaseq
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 60
0
votes
0
replies
1.7k
views
Job: Bioinformatics Researcher - University of Adelaide, South Australia
australia bioinformatician job job Job
10.2 years ago Steve Pederson ▴ 170
2
votes
1
reply
4.4k
views
Dealing with the output of ssGSEA method from GSVA package
gsva ssgsea
10.2 years ago Momeneh Foroutan ▴ 10
0
votes
0
replies
1.8k
views
Job: Senior Bioinformatics Researcher - University of Adelaide, South Australia
bioinformatician job australia veterinary science c++ java Job
10.2 years ago Steve Pederson ▴ 170
0
votes
1
reply
1.8k
views
Extract methylation data from a FirehoseData
RTCGAToolbox
updated 10.2 years ago by • 0 • written 10.2 years ago by • 0
0
votes
0
replies
1.2k
views
RADseq chromosomes unknown
snprelate RADseq Stacks
10.2 years ago clive.darwell • 0
46,726 results • Page 427 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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