Showing : Differential Expression • reset
3
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4
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2.9k
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Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.0k • written 6.3 years ago by • 0
0
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17
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3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
3
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3
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3.3k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.2 years ago by ▴ 30
3
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2
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1.4k
views
Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 3.7 years ago by 50k • written 3.7 years ago by • 0
5
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3
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1.3k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 20
3
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1
reply
1.0k
views
Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 160
6
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5
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2.2k
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
3.9 years ago hollandademello ▴ 20
1
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1
reply
1.6k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by • 0
0
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4
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1.3k
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 4.0 years ago by 50k • written 4.1 years ago by • 0
2
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2
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678
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 20
0
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0
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686
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.1 years ago raquelponti • 0
0
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1
reply
660
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 40
4
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7
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1.1k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 60
7
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4
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4.1k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
2
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1
reply
626
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
4.4 years ago Beginner • 0
2
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3
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1.4k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 180
0
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1
reply
760
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
4.4 years ago A • 0
0
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0
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1.4k
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
4.5 years ago fawazfebin ▴ 60
8
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11
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2.3k
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 4.5 years ago by 50k • written 4.5 years ago by ▴ 20
5
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8
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1.7k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.5 years ago by ★ 13k • written 4.5 years ago by ▴ 30
3
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2
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1.8k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 4.6 years ago by 41k • written 4.6 years ago by ▴ 10
5
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6
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1.2k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.6 years ago by ▴ 840 • written 4.6 years ago by ▴ 10
0
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1
reply
1.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.6 years ago Andrew_McDavid ▴ 270
22
votes
17
replies
7.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 2.9 years ago by 41k • written 5.8 years ago by ▴ 30
2
votes
4
replies
1.2k
views
Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
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1
reply
981
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 4.8 years ago by 41k • written 4.9 years ago by ▴ 40
4
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4
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1.3k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
1
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12
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1.3k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 90
4
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5
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3.2k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 10
1
vote
1
reply
868
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 5.0 years ago by 65k • written 5.0 years ago by • 0
0
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1
reply
1.1k
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
5.1 years ago baldissera152 • 0
5
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1
reply
1.2k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
0
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3
replies
1.4k
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 5.3 years ago by ▴ 10 • written 5.3 years ago by • 0
1
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1
reply
1.3k
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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
5.3 years ago krassowski.michal ▴ 40
2
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7
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2.1k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.6 years ago by 50k • written 5.6 years ago by • 0
15
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12
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2.5k
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 5.7 years ago by 41k • written 5.7 years ago by ▴ 60
1
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3
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1.4k
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 5.8 years ago by ▴ 950 • written 5.8 years ago by • 0
1
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4
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1.5k
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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 5.8 years ago by 65k • written 5.8 years ago by ▴ 40
5
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1
reply
1.0k
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
0
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4
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1.4k
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
1
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4
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1.2k
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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 5.8 years ago by 41k • written 5.8 years ago by ▴ 50
0
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0
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973
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pair wise ballgown
ballgown differential expression
5.8 years ago zoe.ward • 0
0
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0
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1.2k
views
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
5.9 years ago manuelmendoza • 0
1
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6
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1.3k
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
5.9 years ago aec ▴ 90
0
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1
reply
946
views
Interpretation of p-value plot
p values differential expression limma
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
5
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4
replies
1.2k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
0
votes
3
replies
881
views
interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 90
6
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4
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1.4k
views
Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 6.1 years ago by ★ 7.9k • written 6.1 years ago by ▴ 10
7
votes
10
replies
5.7k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 6.1 years ago by ▴ 30 • written 7.7 years ago by ▴ 50
7
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11
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2.5k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 60
50 results • Page 1 of 1
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Comment: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
Or that. ;-D
Answer: Error retrieving ensembl gene id using biomaRt... by Mike Smith ★ 6.5k
I think you have the assignment operator (`<-`) the wrong way round. It should be `df_biomrt_tmp <- getBM(...`
Answer: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value by Michael Love 41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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