0
votes
26
replies
2.3k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
15 months ago • updated 1 hour ago Poonam • 0
0
votes
6
replies
168
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 16 hours ago by ★ 1.3k • written 2 days ago by ▴ 130
1
vote
2
replies
299
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 22 hours ago by 50k • written 1 day ago by • 0
0
votes
1
reply
61
views
package goseq seems to be not available on the latest version of R
goseq
updated 23 hours ago by 50k • written 1 day ago by • 0
2
votes
2
replies
110
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
0
replies
39
views
Handling multiple differential expression comparisons
DESeq2
1 day ago Zainab • 0
0
votes
0
replies
34
views
dba.plotProfile() plotting and interpretation
DiffBind
1 day ago Henry ▴ 10
0
votes
1
reply
85
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 2 days ago by • 0
0
votes
1
reply
82
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 1 day ago by 50k • written 2 days ago by • 0
1
vote
1
reply
196
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 day ago by 50k • written 2 days ago by ▴ 10
0
votes
0
replies
33
views
flowStats for CyTOF
flowStats
2 days ago tholmes • 0
0
votes
2
replies
78
views
DESeq2 v1.35.0
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
0
replies
38
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
2 days ago yvonneh • 0
0
votes
0
replies
31
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago Ian D. ▴ 70
0
votes
1
reply
43
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by • 0
0
votes
2
replies
111
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago Ian D. ▴ 70
0
votes
2
replies
113
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
3 days ago • updated 1 day ago kcarey • 0
0
votes
3
replies
113
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
0
votes
1
reply
121
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
3
votes
0
replies
56
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
3 days ago shepherl 3.9k
0
votes
0
replies
72
views
Empty table plot using plotGseaTable()
fgsea
3 days ago • updated 1 day ago Chris • 0
0
votes
3
replies
139
views
Store output of matchPWM()
biostrings Biostrings
updated 3 days ago by 65k • written 3 days ago by ▴ 70
0
votes
3
replies
233
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
0
votes
2
replies
211
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
3 days ago • updated 2 days ago Yveto • 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 3 days ago by ▴ 200 • written 6.7 years ago by ▴ 80
0
votes
1
reply
215
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 4 days ago by 65k • written 4 days ago by • 0
3
votes
4
replies
191
views
Help with error using camera() in limma
CAMERA limma
4 days ago Chris • 0
1
vote
1
reply
94
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
2
replies
109
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
4 days ago • updated 1 day ago Aurora • 0
0
votes
1
reply
93
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
0
replies
55
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
4 days ago Maria Doyle ▴ 70
0
votes
1
reply
72
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 4 days ago by 3.9k • written 4 days ago by • 0
0
votes
1
reply
94
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
2
votes
2
replies
180
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
5 days ago Chris • 0
0
votes
3
replies
227
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 4 days ago by 65k • written 5 days ago by • 0
0
votes
0
replies
64
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 days ago Chris • 0
3
votes
3
replies
210
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 5 days ago by ★ 4.1k • written 5 days ago by ▴ 10
0
votes
0
replies
112
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
9 days ago • updated 1 day ago glaciya2018 • 0
0
votes
0
replies
79
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 days ago • updated 5 days ago Sara • 0
0
votes
2
replies
155
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 days ago by • 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
14 days ago • updated 3 days ago Chris • 0
0
votes
3
replies
160
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 4 days ago by ★ 1.9k • written 16 days ago by • 0
1
vote
2
replies
283
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 1 day ago Kim • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 4 days ago Chris • 0
0
votes
4
replies
242
views
Minfi - estimatecellscount
min minfi
updated 5 days ago by 65k • written 5 weeks ago by • 0
1
vote
4
replies
474
views
DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 3 days ago JKim • 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 2 days ago by 65k • written 2.3 years ago by • 0
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 4 days ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 4 days ago by • 0 • written 7.9 years ago by • 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 4 days ago by • 0 • written 13.0 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
United States, 8 minutes ago
WEHI, Melbourne, Australia, 19 minutes ago
United States, 38 minutes ago
France, 50 minutes ago
The city by the bay, 1 hour ago
Traffic: 579 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6