0
votes
6
replies
152
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 8 hours ago by ★ 1.3k • written 1 day ago by ▴ 130
1
vote
2
replies
254
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 13 hours ago by 50k • written 17 hours ago by • 0
0
votes
1
reply
49
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 hours ago by 50k • written 18 hours ago by • 0
2
votes
2
replies
100
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 19 hours ago by 41k • written 19 hours ago by • 0
0
votes
0
replies
31
views
Handling multiple differential expression comparisons
DESeq2
20 hours ago Zainab • 0
0
votes
0
replies
29
views
dba.plotProfile() plotting and interpretation
DiffBind
21 hours ago • updated 20 hours ago Henry ▴ 10
0
votes
1
reply
81
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
0
votes
1
reply
77
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 1 day ago by 50k • written 1 day ago by • 0
0
votes
1
reply
168
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 1 day ago by 50k • written 1 day ago by ▴ 10
0
votes
0
replies
29
views
flowStats for CyTOF
flowStats
1 day ago tholmes • 0
0
votes
2
replies
74
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
0
replies
36
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
1 day ago yvonneh • 0
0
votes
0
replies
28
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
1 day ago Ian D. ▴ 70
0
votes
1
reply
40
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by • 0
0
votes
2
replies
105
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 1 day ago Ian D. ▴ 70
0
votes
2
replies
107
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago kcarey • 0
0
votes
3
replies
110
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
1
reply
119
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
3
votes
0
replies
51
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
2 days ago shepherl 3.9k
0
votes
0
replies
70
views
Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 17 hours ago Chris • 0
0
votes
3
replies
133
views
Store output of matchPWM()
biostrings Biostrings
updated 2 days ago by 65k • written 2 days ago by ▴ 70
0
votes
3
replies
231
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
2
replies
206
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
214
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 3 days ago by 65k • written 4 days ago by • 0
3
votes
4
replies
189
views
Help with error using camera() in limma
CAMERA limma
3 days ago Chris • 0
1
vote
1
reply
93
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
108
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
4 days ago • updated 1 day ago Aurora • 0
0
votes
1
reply
92
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
0
replies
51
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
4 days ago Maria Doyle ▴ 70
0
votes
1
reply
70
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
93
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
176
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
4 days ago Chris • 0
0
votes
3
replies
223
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 3 days ago by 65k • written 4 days ago by • 0
0
votes
0
replies
63
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
4 days ago Chris • 0
3
votes
3
replies
206
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
1
vote
1
reply
112
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 7 days ago by ▴ 40 • written 8 days ago by ★ 1.5k
0
votes
2
replies
192
views
PCA plot suggestions
DESeq2 PCAtools
updated 7 days ago by 41k • written 9 days ago by • 0
1
vote
3
replies
200
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 8 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
123
views
ATACseq merge peaks
DiffBind
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
1
vote
1
reply
159
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 8 days ago by 50k • written 12 days ago by ▴ 730
1
vote
7
replies
305
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
8 days ago • updated 7 days ago pl23 • 0
2
votes
9
replies
358
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 days ago by 65k • written 9 days ago by • 0
0
votes
0
replies
105
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
1
vote
2
replies
150
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
10 days ago • updated 9 days ago ATpoint ★ 4.1k
0
votes
1
reply
142
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 days ago by 41k • written 9 days ago by • 0
0
votes
0
replies
78
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
9 days ago • updated 5 days ago Sara • 0
2
votes
5
replies
249
views
get BM error
ensembldb
updated 9 days ago by 65k • written 10 days ago by • 0
2
votes
5
replies
228
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 8 days ago by 65k • written 10 days ago by • 0
0
votes
0
replies
78
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago Dario Strbenac ★ 1.5k
201 results • Page 1 of 5
Recent ...
Replies
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…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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
Taiwan, 3 minutes ago
Ireland, 7 minutes ago
United States, 11 minutes ago
France, 21 minutes ago
WEHI, Melbourne, Australia, 46 minutes ago
Traffic: 557 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