Showing : DifferentialExpression • reset
9
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13
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6.4k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
6
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11
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
4
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10
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1.3k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.5 years ago Hajar • 0
5
votes
9
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1.5k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 830
3
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8
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3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 24 months ago by ▴ 10
0
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8
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798
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
5 months ago Luca • 0
1
vote
8
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1.6k
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edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
22 months ago giBio • 0
1
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8
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1.5k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 10 months ago by • 0
1
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8
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1.7k
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
2.3 years ago dadca596 • 0
0
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8
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1.3k
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Swish log2FC NA output
swish fishpond DifferentialExpression
21 months ago jvandinter • 0
0
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8
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1.4k
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Three conditions and two time points
DifferentialExpression DESeq2 time
2.6 years ago • updated 2.5 years ago AZ ▴ 30
2
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8
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2.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
0
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7
replies
1.2k
views
Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 17 months ago by 65k • written 18 months ago by • 0
3
votes
7
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1.5k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 17 months ago by 50k • written 18 months ago by • 0
0
votes
7
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2.3k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 3.4 years ago by 50k • written 3.5 years ago by ▴ 20
0
votes
7
replies
1.2k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
2.0 years ago • updated 24 months ago JAcky • 0
2
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7
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2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
0
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7
replies
1.4k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
3
votes
7
replies
1.4k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 30
2
votes
6
replies
943
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.8k • written 11 months ago by • 0
5
votes
6
replies
391
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 11 days ago by ★ 4.0k • written 15 days ago by ▴ 30
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
0
votes
6
replies
757
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
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6
replies
1.2k
views
Error while running DESeq2
DifferentialExpression
22 months ago srikar • 0
3
votes
6
replies
1.3k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 14 months ago by 50k • written 14 months ago by • 0
5
votes
6
replies
526
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
4
votes
6
replies
554
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
votes
6
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2.2k
views
Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
4.6 years ago • updated 2.3 years ago hermidalc ▴ 20
2
votes
6
replies
753
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
3
votes
6
replies
1.4k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 17 months ago by • 0
3
votes
6
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1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
0
votes
6
replies
880
views
DESeq2 time course confusion
DESeq2 DifferentialExpression
2.8 years ago rajpal22288 ▴ 10
0
votes
5
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595
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 12 weeks ago Lucy ▴ 60
4
votes
5
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1.7k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 24 months ago by • 0 • written 2.2 years ago by ▴ 30
0
votes
5
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1.2k
views
DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 19 months ago by 41k • written 2.7 years ago by • 0
0
votes
5
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1.6k
views
Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 2.2 years ago by 41k • written 2.2 years ago by ▴ 10
3
votes
5
replies
4.7k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.6 years ago zhxiaokang ▴ 20
0
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4
replies
730
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
0
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4
replies
1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
0
votes
4
replies
272
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago • updated 7 weeks ago mperalc • 0
3
votes
4
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1.3k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.0 years ago mohammedtoufiq91 ▴ 10
2
votes
4
replies
805
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 15 months ago by 41k • written 15 months ago by • 0
0
votes
4
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1.0k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
22 months ago S • 0
3
votes
4
replies
393
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by ▴ 50
1
vote
4
replies
914
views
How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 23 months ago by ★ 3.9k • written 23 months ago by • 0
4
votes
4
replies
7.2k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
1
vote
4
replies
535
views
rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 5 months ago by 41k • written 5 months ago by ▴ 60
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
2
votes
4
replies
488
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
2
votes
4
replies
652
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago • updated 6 months ago Shihui • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: Adding a group of samples reduces DEGs in other groups
Answer: Gene set analysis: GSVA, Z-Score, and fold-changes
Answer: FilterByExpr low counts with small sample size
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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