1
vote
2
replies
372
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 9 days ago by 50k • written 9 days ago by • 0
0
votes
0
replies
127
views
Empty table plot using plotGseaTable()
fgsea
11 days ago • updated 9 days ago Chris ▴ 10
1
vote
2
replies
338
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
5 weeks ago • updated 9 days ago Kim • 0
0
votes
0
replies
104
views
dba.plotProfile() plotting and interpretation
DiffBind
9 days ago Henry ▴ 10
0
votes
2
replies
150
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
13 days ago • updated 10 days ago Aurora • 0
0
votes
0
replies
132
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
18 days ago • updated 10 days ago glaciya2018 • 0
0
votes
2
replies
187
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago kcarey • 0
0
votes
1
reply
155
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 10 days ago by 50k • written 10 days ago by • 0
0
votes
1
reply
138
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 10 days ago by 50k • written 10 days ago by • 0
0
votes
0
replies
84
views
flowStats for CyTOF
flowStats
10 days ago tholmes • 0
0
votes
2
replies
140
views
DESeq2 v1.35.0
DESeq2
updated 11 days ago by 42k • written 11 days ago by • 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 11 days ago by 65k • written 2.3 years ago by • 0
0
votes
0
replies
78
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
11 days ago yvonneh • 0
0
votes
0
replies
73
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
11 days ago Ian D. ▴ 70
0
votes
1
reply
114
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 11 days ago by • 0
0
votes
3
replies
194
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
0
votes
2
replies
178
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 20 days ago by • 0
1
vote
2
replies
266
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
12 days ago • updated 11 days ago Yveto • 0
0
votes
3
replies
283
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by 42k • written 12 days ago by • 0
4
votes
0
replies
118
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
11 days ago shepherl 3.9k
15
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
23 days ago • updated 11 days ago Chris ▴ 10
0
votes
3
replies
200
views
Store output of matchPWM()
biostrings Biostrings
updated 11 days ago by 65k • written 12 days ago by ▴ 70
1
vote
4
replies
500
views
DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 11 days ago JKim • 0
3
votes
4
replies
245
views
Help with error using camera() in limma
CAMERA limma
13 days ago • updated 12 days ago Chris ▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 12 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 12 days ago by • 0 • written 13.1 years ago by ▴ 10
0
votes
1
reply
253
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 12 days ago by 65k • written 13 days ago by • 0
0
votes
3
replies
261
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 13 days ago by 65k • written 14 days ago by • 0
15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
6 weeks ago • updated 13 days ago Chris ▴ 10
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 13 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
3
replies
178
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 13 days ago by ★ 1.9k • written 25 days ago by • 0
1
vote
1
reply
140
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
1
reply
126
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
0
replies
84
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
13 days ago Maria Doyle ▴ 70
0
votes
1
reply
111
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 13 days ago by 3.9k • written 13 days ago by • 0
0
votes
1
reply
126
views
putting my own expression data in deseq2
DESeq2
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
2
votes
2
replies
218
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
13 days ago Chris ▴ 10
0
votes
0
replies
86
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
14 days ago • updated 13 days ago Chris ▴ 10
0
votes
4
replies
256
views
Minfi - estimatecellscount
min minfi
updated 14 days ago by 65k • written 6 weeks ago by • 0
3
votes
3
replies
255
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 14 days ago by ★ 4.1k • written 14 days ago by ▴ 10
0
votes
0
replies
94
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
19 days ago • updated 14 days ago Sara • 0
1
vote
1
reply
142
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 16 days ago by ▴ 40 • written 17 days ago by ★ 1.5k
1
vote
7
replies
342
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
17 days ago • updated 16 days ago pl23 • 0
0
votes
2
replies
220
views
PCA plot suggestions
DESeq2 PCAtools
updated 17 days ago by 42k • written 18 days ago by • 0
1
vote
2
replies
726
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
26 days ago • updated 17 days ago ussarizona ▴ 10
1
vote
3
replies
240
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 17 days ago by 42k • written 17 days ago by • 0
0
votes
1
reply
155
views
ATACseq merge peaks
DiffBind
updated 17 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
4
replies
347
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago winwater0928 • 0
2
votes
9
replies
408
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 17 days ago by 65k • written 18 days ago by • 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 18 days ago by 65k • written 19 days ago by • 0
190 results • Page 2 of 4
Recent ...
Replies
Comment: Problem finding certain variables when importing a public database GSE73103 by Guido Hooiveld ★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Comment: ChAMP installation issue by shepherl 3.9k
Without showing the commands you tried and the full output including error it is impossible to help. Please provide additional information…
Answer: Gene set enrichment analysis by Guido Hooiveld ★ 3.9k
No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are e…
Votes
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
Why p value inconsistent when using different number of pathway score?
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
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