Showing : DifferentialExpression • reset
9
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13
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6.6k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.1 years ago by ▴ 30
2
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7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
1
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8
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1.6k
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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
0
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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
12 months ago • updated 11 months ago ruba-mahmoud • 0
2
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6
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975
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.9k • written 11 months ago by • 0
3
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3
replies
956
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
0
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8
replies
822
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
0
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6
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782
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
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6
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777
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
0
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2
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748
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
12 months ago António Miguel de Jesus Domingues ▴ 510
0
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4
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746
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
5
votes
3
replies
714
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
2
votes
4
replies
688
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
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2
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685
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
0
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3
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652
views
limma paired design
DifferentialExpression limma
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
2
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650
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
5
replies
621
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
votes
1
reply
608
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 11 months ago by 50k • written 12 months ago by • 0
4
votes
6
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604
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
1
vote
3
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600
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
0
votes
1
reply
590
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 11 months ago by ★ 1.3k • written 11 months ago by • 0
3
votes
3
replies
576
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
1
vote
3
replies
570
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
5
votes
6
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557
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
1
vote
4
replies
556
views
rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 6 months ago by 41k • written 6 months ago by ▴ 60
1
vote
1
reply
533
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
2
replies
530
views
Contrast of Contrasts in Limma
limma DifferentialExpression
12 months ago mpitz • 0
0
votes
2
replies
521
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago • updated 7 months ago Beyza • 0
2
votes
4
replies
518
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
0
votes
1
reply
506
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
0
votes
1
reply
500
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
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0
replies
476
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 41k • written 11 months ago by ▴ 20
0
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3
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459
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
0
replies
440
views
DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 9 months ago by 65k • written 9 months ago by • 0
3
votes
4
replies
433
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 50
0
votes
3
replies
430
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
5
votes
6
replies
430
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 23 days ago by ★ 4.1k • written 27 days ago by ▴ 30
1
vote
2
replies
424
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
1
reply
418
views
''Model_Matrix'' error
DifferentialExpression limma
updated 7 months ago by 50k • written 7 months ago by • 0
1
vote
3
replies
410
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
1
reply
403
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
1
reply
389
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 8 months ago by 65k • written 8 months ago by • 0
2
votes
3
replies
372
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
0
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0
replies
371
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
4
votes
3
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359
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
1
reply
347
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 41k • written 5 months ago by ▴ 10
0
votes
2
replies
347
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
0
votes
2
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324
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 7 weeks ago by 41k • written 7 weeks ago by • 0
2
votes
1
reply
304
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
0
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4
replies
304
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea() by James W. MacDonald 65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea() by James W. MacDonald 65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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