18
votes
24
replies
14k
views
[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 3.2 years ago by • 0 • written 9.1 years ago by ▴ 120
18
votes
17
replies
4.0k
views
How to model a comparison between comparisons in edgeR?
edger rnaseq
updated 9.1 years ago by ★ 7.9k • written 9.1 years ago by ▴ 60
18
votes
10
replies
7.0k
views
Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 8.1 years ago by 50k • written 8.2 years ago by ▴ 170
18
votes
4
replies
1.6k
views
`ggbio` package can't be loaded
ggbio
3.3 years ago Batool ▴ 370
18
votes
12
replies
3.7k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 8.9 years ago by 41k • written 8.9 years ago by ★ 7.9k
17
votes
7
replies
11k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 6.2 years ago by 65k • written 6.2 years ago by ▴ 150
17
votes
7
replies
5.9k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7.9 years ago by ★ 7.9k • written 7.9 years ago by ▴ 10
17
votes
8
replies
3.1k
views
How to check the read length for all the TCGA data samples in GDC?
gdc tcga wes gdc data
updated 6.0 years ago by 21k • written 6.0 years ago by ▴ 110
17
votes
5
replies
4.1k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 7.1 years ago by 25k • written 7.1 years ago by ▴ 20
17
votes
4
replies
8.9k
views
Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
updated 29 days ago by • 0 • written 5.2 years ago by 3.8k
17
votes
14
replies
40k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 22 months ago by • 0 • written 6.8 years ago by ▴ 20
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.7 years ago by • 0 • written 13.5 years ago by ▴ 120
17
votes
7
replies
13k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger rnaseq differential expression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 150
17
votes
4
replies
16k
views
How to properly sort GRanges?
granges genomicranges sort seqnames order
updated 9.0 years ago by ▴ 30 • written 9.5 years ago by ▴ 660
17
votes
9
replies
32k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 3.3 years ago by 41k • written 8.2 years ago by ▴ 100
17
votes
5
replies
4.7k
views
limma voom Mean-variance trend plot: x-axis?
limma
5.0 years ago AS ▴ 70
16
votes
5
replies
7.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma voom deseq normalization ercc
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 120
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 6.5 years ago by ★ 5.2k • written 8.1 years ago by ▴ 60
16
votes
4
replies
11k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 8.6 years ago by ★ 11k • written 8.6 years ago by ▴ 50
16
votes
0
replies
3.7k
views
simultaneous use of robust and weighting methods in limma
limma robust arrayWeights
10.4 years ago • updated 7.9 years ago Gordon Smyth 50k
16
votes
12
replies
2.3k
views
VST transformation (DESeq2) for metabolomics data
vst Metabolomics DESeq2
2.0 years ago • updated 24 months ago Joan Miró ▴ 80
16
votes
13
replies
16k
views
deseq2 normalized data with heatmap
deseq2
updated 2.8 years ago by ▴ 10 • written 3.7 years ago by ▴ 20
16
votes
5
replies
14k
views
Error: Bioconductor version '3.8' requires R version '3.5'
software error
updated 5.0 years ago by ★ 6.5k • written 5.0 years ago by ▴ 10
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
16
votes
40
replies
8.5k
views
Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 2.3 years ago by • 0 • written 4.7 years ago by ▴ 50
16
votes
10
replies
6.6k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 14 months ago by 16k • written 2.5 years ago by ▴ 20
16
votes
13
replies
4.3k
views
Camera and ROAST
limma
updated 6.4 years ago by 50k • written 6.4 years ago by ▴ 30
15
votes
2
replies
17k
views
Extract sequence from DNAStringSet object
dnastringset
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 120
15
votes
9
replies
13k
views
Best way to convert uniprot accessions to entrez gene identifiers in R
org.hs.eg.db uniprot accessions entrez gene identifiers
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 160
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma microarray
updated 9.2 years ago by 21k • written 9.3 years ago by ▴ 340
15
votes
6
replies
29k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR cpm
updated 5.9 years ago by ▴ 20 • written 6.1 years ago by ▴ 40
15
votes
4
replies
2.7k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by ▴ 130
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
26 days ago • updated 4 days ago Chris • 0
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
15
votes
12
replies
66k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 120
15
votes
12
replies
2.5k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 60
15
votes
6
replies
3.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 7.7 years ago by ▴ 90 • written 7.7 years ago by ▴ 170
15
votes
3
replies
1.6k
views
lfcShrink function for different comparison
DESeq2 RNASeq
updated 2.2 years ago by ▴ 30 • written 3.5 years ago by ▴ 90
15
votes
13
replies
3.0k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 2.5 years ago by ▴ 10 • written 2.5 years ago by ▴ 20
15
votes
18
replies
3.3k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 60
15
votes
4
replies
32k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 3.7 years ago by ▴ 190 • written 3.7 years ago by ▴ 10
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges grangeslist granges s4
updated 2.1 years ago by 16k • written 7.9 years ago by ▴ 40
15
votes
8
replies
11k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2 deseq
9.5 years ago • updated 9.4 years ago salahm ▴ 70
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.4 years ago Deleted ▴ 70
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
7.9 years ago giroudpaul ▴ 40
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2 annotation granges
updated 2.2 years ago by ▴ 60 • written 9.5 years ago by ▴ 120
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA Hub Genes KmE Intramodular Connectivity
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by ▴ 150
14
votes
12
replies
9.3k
views
limma lmFit coefficients and p-values
limma methylation ewas
updated 7.7 years ago by ★ 13k • written 7.7 years ago by ▴ 30
14
votes
4
replies
29k
views
heatmap.2() get matrix after hierarchical clustering
Clustering Clustering
updated 11.5 years ago by ★ 1.7k • written 11.5 years ago by ★ 13k
1,000 results • Page 2 of 20
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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