Showing : differential expression • reset
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Protein differential Expression analysis
differential expression proteomics
updated 20 months ago by ★ 4.8k • written 7.3 years ago by • 0
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17
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4.4k
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 22 months ago by • 0 • written 7.6 years ago by • 0
3
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3
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.1 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
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2
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2.2k
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 4.7 years ago by 52k • written 4.7 years ago by • 0
5
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3
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1.9k
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Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 20
3
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1
reply
1.4k
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Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 180
6
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7
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3.5k
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 3 months ago by 52k • written 4.9 years ago by ▴ 20
1
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1
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2.2k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
0
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4
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1.7k
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 5.0 years ago by 52k • written 5.1 years ago by • 0
2
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949
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 5.0 years ago by 52k • written 5.0 years ago by ▴ 20
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0
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933
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
5.1 years ago raquelponti • 0
0
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1
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895
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 40
4
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7
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1.6k
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'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 5.1 years ago by 68k • written 5.1 years ago by ▴ 60
7
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4
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Limma when to use zero intercept
limma regression differential expression linear model
updated 5.2 years ago by 52k • written 5.2 years ago by • 0
2
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1
reply
818
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Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
5.4 years ago Beginner • 0
2
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3
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1.7k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 180
0
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1
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1.1k
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
5.5 years ago A • 0
0
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0
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1.8k
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
5.5 years ago fawazfebin ▴ 60
9
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11
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3.3k
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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 5.5 years ago by 52k • written 5.6 years ago by ▴ 20
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8
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2.3k
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Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 5.6 years ago by ★ 13k • written 5.6 years ago by ▴ 30
3
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2
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 10
5
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6
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1.7k
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is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 5.6 years ago by ▴ 900 • written 5.6 years ago by ▴ 10
0
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1
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2.4k
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.6 years ago Andrew_McDavid ▴ 280
27
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17
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9.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.9 years ago by 43k • written 6.8 years ago by ▴ 50
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4
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1.7k
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Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
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1
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1.2k
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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 5.9 years ago by 43k • written 5.9 years ago by ▴ 40
4
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4
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1.8k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 40
1
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12
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1.9k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 90
4
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5
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5.6k
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How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 10
1
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1
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1.2k
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 6.0 years ago by 68k • written 6.0 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
6.1 years ago baldissera152 • 0
5
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1
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1.6k
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Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
0
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3
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1.9k
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 6.3 years ago by ▴ 10 • written 6.3 years ago by • 0
1
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1
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1.6k
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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
6.3 years ago krassowski.michal ▴ 40
2
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7
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2.8k
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Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
15
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12
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3.1k
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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 6.7 years ago by 43k • written 6.7 years ago by ▴ 60
2
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3
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1.9k
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 6.8 years ago by ▴ 980 • written 6.8 years ago by • 0
1
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4
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1.9k
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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 6.8 years ago by 68k • written 6.8 years ago by ▴ 60
5
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1
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1.3k
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
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4
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1.8k
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
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4
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1.6k
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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 6.8 years ago by 43k • written 6.8 years ago by ▴ 50
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0
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1.2k
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pair wise ballgown
ballgown differential expression
6.8 years ago zoe.ward • 0
0
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0
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
6.9 years ago manuelmendoza • 0
1
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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
7.0 years ago aec ▴ 90
0
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1
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1.2k
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Interpretation of p-value plot
p values differential expression limma
updated 7.0 years ago by 52k • written 7.0 years ago by • 0
5
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4
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1.6k
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Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 7.0 years ago by 52k • written 7.0 years ago by • 0
0
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3
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1.1k
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interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 90
6
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4
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1.9k
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Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 7.1 years ago by ★ 7.9k • written 7.1 years ago by ▴ 10
7
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10
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7.2k
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Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 7.1 years ago by ▴ 30 • written 8.7 years ago by ▴ 50
7
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11
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3.1k
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Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 7.1 years ago by 52k • written 7.1 years ago by ▴ 60
50 results • Page 1 of 1
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Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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