Showing : DifferentialExpression • reset
9
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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 2.2 years ago by ▴ 30
1
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8
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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 11 months ago by • 0
0
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8
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836
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
2
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7
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3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
2
votes
7
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336
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
7 days ago • updated 4 days ago sajadahmad41454 • 0
2
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6
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989
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How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.9k • written 11 months ago by • 0
5
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6
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593
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
0
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6
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800
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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
4
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6
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631
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
2
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6
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792
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
5
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6
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451
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
0
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5
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637
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
2
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4
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541
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 4 months ago by • 0
3
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4
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484
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
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4
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319
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago • updated 10 weeks ago mperalc • 0
0
votes
4
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755
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
1
vote
4
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570
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 6 months ago by 42k • written 6 months ago by ▴ 60
2
votes
4
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717
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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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
12 months ago ruba-mahmoud • 0
1
vote
3
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202
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 19 hours ago by 50k • written 1 day ago by • 0
5
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3
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729
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
0
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3
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74
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 8 hours ago by 42k • written 1 day ago by • 0
2
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3
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383
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
4
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3
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372
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
3
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606
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
3
votes
3
replies
970
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by ▴ 20
0
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3
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674
views
limma paired design
DifferentialExpression limma
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
3
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463
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
3
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274
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
votes
3
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435
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
3
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583
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
3
votes
3
replies
585
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
0
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3
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269
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 15 days ago by 65k • written 16 days ago by • 0
0
votes
3
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204
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
1
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3
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435
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
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2
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317
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by • 0
0
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2
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346
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 8 weeks ago by 42k • written 9 weeks ago by • 0
3
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2
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311
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
0
votes
2
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240
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 30
0
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2
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530
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
1
vote
2
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449
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
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2
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699
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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2
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369
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
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2
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299
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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2
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180
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
vote
2
replies
247
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
7 weeks ago Chanderkant Chaudhary • 0
0
votes
1
reply
604
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 ★ 1.4k • written 11 months ago by • 0
1
vote
1
reply
549
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 10 months ago by 50k • written 10 months ago by • 0
0
votes
1
reply
509
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
3
votes
1
reply
322
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
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Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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