Showing : Differential expression • reset
3
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4
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Protein differential Expression analysis
differential expression proteomics
updated 17 months ago by ★ 4.6k • written 7.1 years ago by • 0
0
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17
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4.1k
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 19 months ago by • 0 • written 7.3 years ago by • 0
3
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3
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4.1k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.9 years ago by ▴ 30 • written 6.0 years ago by ▴ 40
4
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2
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1.9k
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
5
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3
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1.7k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 20
3
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1
reply
1.3k
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Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 160
6
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7
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3.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 24 days ago by 52k • written 4.7 years ago by ▴ 20
1
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1
reply
2.0k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
0
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4
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1.6k
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
2
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2
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868
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 4.8 years ago by 52k • written 4.8 years ago by ▴ 20
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0
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874
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.8 years ago raquelponti • 0
0
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1
reply
844
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 40
4
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7
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1.5k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.8 years ago by 67k • written 4.8 years ago by ▴ 60
7
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4
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5.8k
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Limma when to use zero intercept
limma regression differential expression linear model
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
2
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1
reply
754
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
5.2 years ago • updated 5.1 years ago Beginner • 0
2
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3
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1.6k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 180
0
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1
reply
1000
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
5.2 years ago A • 0
0
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0
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1.7k
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
5.3 years ago fawazfebin ▴ 60
9
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11
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3.0k
views
dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 5.3 years ago by 52k • written 5.3 years ago by ▴ 20
5
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8
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2.1k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 5.3 years ago by ★ 13k • written 5.3 years ago by ▴ 30
3
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2
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2.3k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.3 years ago by 43k • written 5.4 years ago by ▴ 10
5
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6
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1.6k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 5.4 years ago by ▴ 900 • written 5.4 years ago by ▴ 10
0
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1
reply
2.1k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.4 years ago Andrew_McDavid ▴ 270
26
votes
17
replies
8.6k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.7 years ago by 43k • written 6.6 years ago by ▴ 40
2
votes
4
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1.6k
views
Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
1
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1
reply
1.1k
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 40
4
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4
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1.7k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 40
1
vote
12
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1.7k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 90
4
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5
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4.9k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 5.7 years ago by 52k • written 5.7 years ago by ▴ 10
1
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1
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1.1k
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
0
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1
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1.3k
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
5.9 years ago baldissera152 • 0
5
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1
reply
1.5k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.9 years ago by 67k • written 5.9 years ago by • 0
0
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3
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1.8k
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 6.0 years ago by ▴ 10 • written 6.0 years ago by • 0
1
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1
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1.5k
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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva plage differential expression gene set enrichment
6.0 years ago krassowski.michal ▴ 40
2
votes
7
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2.6k
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Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 6.4 years ago by 52k • written 6.4 years ago by • 0
15
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12
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2.9k
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 6.4 years ago by 43k • written 6.4 years ago by ▴ 60
2
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3
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1.8k
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 6.5 years ago by ▴ 980 • written 6.5 years ago by • 0
1
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4
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1.8k
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venDiagram after limma showing more genes after specifying up or down regulated specifically
venn diagram venndiagram limma microarray differential expression
updated 6.5 years ago by 67k • written 6.5 years ago by ▴ 40
5
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1
reply
1.2k
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
0
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4
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1.7k
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
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4
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1.5k
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DE analysis of orthologs with varying sequence lengths using RSEM+tximport+DEseq2: normalization for sequence length?
deseq2 sequence length normalization RSEM tximport differential expression
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 50
0
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0
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1.2k
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pair wise ballgown
ballgown differential expression
6.6 years ago zoe.ward • 0
0
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0
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1.4k
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
6.6 years ago manuelmendoza • 0
1
vote
6
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1.6k
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.7 years ago aec ▴ 90
0
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1
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1.1k
views
Interpretation of p-value plot
p values differential expression limma
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
5
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4
replies
1.5k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
0
votes
3
replies
1.1k
views
interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 90
6
votes
4
replies
1.7k
views
Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 6.9 years ago by ★ 7.9k • written 6.9 years ago by ▴ 10
7
votes
10
replies
6.8k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 6.9 years ago by ▴ 30 • written 8.5 years ago by ▴ 50
7
votes
11
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2.9k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 60
50 results • Page 1 of 1
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Answer: Unable to find sample sheet file for ChAMP methylation data analysis by James W. MacDonald 67k
There is an example file in the extdata directory of the `minfiData` package that you could emulate.
Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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