Showing : DifferentialExpression • reset
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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
2
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7
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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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2
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423
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
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2
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282
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
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6
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776
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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
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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
9
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13
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6.5k
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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
1
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3
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408
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
1
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3
replies
599
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
0
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8
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821
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
5
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6
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555
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
1
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4
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554
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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
0
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6
replies
779
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
0
votes
1
reply
345
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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
2
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3
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371
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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1
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499
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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
4
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3
replies
357
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
505
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
3
votes
3
replies
955
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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1
reply
417
views
''Model_Matrix'' error
DifferentialExpression limma
updated 7 months ago by 50k • written 7 months ago by • 0
1
vote
1
reply
402
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
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3
replies
649
views
limma paired design
DifferentialExpression limma
updated 10 months ago by 65k • written 10 months ago by • 0
0
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2
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171
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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3
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457
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
1
vote
3
replies
262
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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3
replies
429
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
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2
replies
323
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 7 weeks ago by 41k • written 7 weeks ago by • 0
1
vote
2
replies
529
views
Contrast of Contrasts in Limma
limma DifferentialExpression
12 months ago mpitz • 0
0
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1
reply
607
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 11 months ago by 50k • written 11 months ago by • 0
0
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2
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747
views
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
3
votes
2
replies
297
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
1
vote
3
replies
569
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
0
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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
0
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1
reply
589
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
2
votes
1
reply
215
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 3 months ago by 41k • written 3 months ago by ▴ 20
5
votes
3
replies
712
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
1
vote
2
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237
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
0
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2
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346
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
vote
2
replies
649
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
1
reply
388
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
0
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2
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684
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
3
votes
4
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432
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
5
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6
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426
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 23 days ago by ★ 4.1k • written 26 days ago by ▴ 30
4
votes
6
replies
602
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
0
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3
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239
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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 5 days ago by 65k • written 6 days ago by • 0
0
votes
2
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297
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 41k • written 3 months ago by • 0
2
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4
replies
687
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
2
votes
1
reply
302
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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2
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220
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 26 days ago by 41k • written 4 weeks ago by ▴ 30
3
votes
3
replies
573
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
50 results • Page 1 of 1
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Comment: Couldn't connect to server while using "pathways" by ATpoint ★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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