0
votes
1
reply
145
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 days ago by 50k • written 8 days ago by • 0
0
votes
1
reply
128
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 8 days ago by 50k • written 8 days ago by • 0
0
votes
0
replies
74
views
flowStats for CyTOF
flowStats
8 days ago tholmes • 0
0
votes
2
replies
130
views
DESeq2 v1.35.0
DESeq2
updated 8 days ago by 42k • written 8 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 8 days ago by 65k • written 2.3 years ago by • 0
0
votes
0
replies
68
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
8 days ago yvonneh • 0
0
votes
0
replies
63
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 days ago Ian D. ▴ 70
0
votes
1
reply
102
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 8 days ago by • 0
0
votes
3
replies
174
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 days ago by ★ 4.1k • written 9 days ago by • 0
0
votes
2
replies
175
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 18 days ago by • 0
1
vote
2
replies
255
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
10 days ago • updated 9 days ago Yveto • 0
0
votes
3
replies
270
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 9 days ago by 42k • written 10 days ago by • 0
4
votes
0
replies
106
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
9 days ago shepherl 3.9k
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
20 days ago • updated 9 days ago Chris • 0
0
votes
3
replies
188
views
Store output of matchPWM()
biostrings Biostrings
updated 9 days ago by 65k • written 9 days ago by ▴ 70
1
vote
4
replies
495
views
DEseq2 coefficient
DESeq2 coefficient
11 weeks ago • updated 9 days ago JKim • 0
3
votes
4
replies
238
views
Help with error using camera() in limma
CAMERA limma
10 days ago Chris • 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 10 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 10 days ago by • 0 • written 13.0 years ago by ▴ 10
0
votes
1
reply
244
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 10 days ago by 65k • written 11 days ago by • 0
0
votes
3
replies
257
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 10 days ago by 65k • written 11 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 10 days ago Chris • 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 10 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
3
replies
177
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 days ago by ★ 1.9k • written 22 days ago by • 0
1
vote
1
reply
135
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 10 days ago by 42k • written 10 days ago by • 0
0
votes
1
reply
121
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 10 days ago by 42k • written 11 days ago by • 0
0
votes
0
replies
82
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
10 days ago Maria Doyle ▴ 70
0
votes
1
reply
108
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 10 days ago by 3.9k • written 11 days ago by • 0
0
votes
1
reply
123
views
putting my own expression data in deseq2
DESeq2
updated 10 days ago by ★ 4.1k • written 10 days ago by • 0
2
votes
2
replies
215
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
11 days ago Chris • 0
0
votes
0
replies
84
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
11 days ago Chris • 0
0
votes
4
replies
255
views
Minfi - estimatecellscount
min minfi
updated 11 days ago by 65k • written 6 weeks ago by • 0
3
votes
3
replies
250
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 11 days ago by ★ 4.1k • written 12 days ago by ▴ 10
0
votes
0
replies
94
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
16 days ago • updated 12 days ago Sara • 0
1
vote
1
reply
140
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 14 days ago by ▴ 40 • written 14 days ago by ★ 1.5k
1
vote
7
replies
341
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
15 days ago • updated 14 days ago pl23 • 0
0
votes
2
replies
216
views
PCA plot suggestions
DESeq2 PCAtools
updated 14 days ago by 42k • written 16 days ago by • 0
1
vote
2
replies
722
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
23 days ago • updated 14 days ago ussarizona ▴ 10
1
vote
3
replies
236
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 14 days ago by 42k • written 15 days ago by • 0
0
votes
1
reply
152
views
ATACseq merge peaks
DiffBind
updated 14 days ago by ★ 4.1k • written 16 days ago by • 0
1
vote
4
replies
345
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
17 days ago • updated 15 days ago winwater0928 • 0
2
votes
9
replies
406
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 15 days ago by 65k • written 15 days ago by • 0
2
votes
5
replies
250
views
How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 15 days ago by 65k • written 17 days ago by • 0
1
vote
2
replies
167
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
16 days ago ATpoint ★ 4.1k
0
votes
2
replies
259
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
18 days ago • updated 16 days ago shuwangxinze1996 • 0
0
votes
8
replies
362
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 16 days ago by ★ 1.4k • written 17 days ago by • 0
0
votes
1
reply
160
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 16 days ago by 42k • written 16 days ago by • 0
2
votes
13
replies
451
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
19 days ago • updated 16 days ago fernanda.backsouza ▴ 10
2
votes
5
replies
283
views
get BM error
ensembldb
updated 16 days ago by 65k • written 17 days ago by • 0
0
votes
5
replies
307
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb AnnotationForge
updated 16 days ago by 65k • written 19 days ago by • 0
1,000 results • Page 2 of 20
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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