Showing : Differential expression • reset
3
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4
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3.5k
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Protein differential Expression analysis
differential expression proteomics
updated 16 months ago by ★ 4.6k • written 7.0 years ago by • 0
0
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17
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4.1k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 18 months ago by • 0 • written 7.2 years ago by • 0
3
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3
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4.0k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.8 years ago by ▴ 30 • written 5.9 years ago by ▴ 40
4
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2
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1.9k
views
Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 4.3 years ago by 52k • written 4.3 years ago by • 0
5
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3
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1.6k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 20
3
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1
reply
1.3k
views
Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 160
6
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5
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2.9k
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.6 years ago hollandademello ▴ 20
1
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1
reply
1.9k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 4.6 years ago by ★ 4.0k • written 4.6 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 4.7 years ago by 52k • written 4.7 years ago by • 0
2
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2
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856
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 4.7 years ago by 52k • written 4.7 years ago by ▴ 20
0
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0
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856
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.7 years ago raquelponti • 0
0
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1
reply
830
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 40
4
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7
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1.4k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.7 years ago by 67k • written 4.7 years ago by ▴ 60
7
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4
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5.6k
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Limma when to use zero intercept
limma regression differential expression linear model
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
2
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1
reply
736
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
5.1 years ago • updated 5.0 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 5.1 years ago by 43k • written 5.1 years ago by ▴ 180
0
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1
reply
979
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
5.1 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
5.2 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 5.2 years ago by 52k • written 5.2 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 5.2 years ago by ★ 13k • written 5.2 years ago by ▴ 30
3
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2
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2.2k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.2 years ago by 43k • written 5.3 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 5.3 years ago by ▴ 900 • written 5.3 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
5.3 years ago Andrew_McDavid ▴ 270
26
votes
17
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8.4k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.6 years ago by 43k • written 6.5 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 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
1
vote
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 5.5 years ago by 43k • written 5.5 years ago by ▴ 40
4
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4
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1.6k
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 40
1
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12
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1.6k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 90
4
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5
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4.7k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 10
1
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1
reply
1.1k
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
0
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1
reply
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
5.8 years ago baldissera152 • 0
5
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1
reply
1.5k
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Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
0
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3
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1.7k
views
How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 5.9 years ago by ▴ 10 • written 5.9 years ago by • 0
1
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1
reply
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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2.5k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 6.3 years ago by 52k • written 6.3 years ago by • 0
15
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12
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2.9k
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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 6.3 years ago by 43k • written 6.3 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 6.4 years ago by ▴ 980 • written 6.4 years ago by • 0
1
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4
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1.7k
views
venDiagram after limma showing more genes after specifying up or down regulated specifically
venn diagram venndiagram limma microarray differential expression
updated 6.4 years ago by 67k • written 6.4 years ago by ▴ 40
5
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1
reply
1.2k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
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4
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1.6k
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 6.5 years ago by 43k • written 6.5 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 6.5 years ago by 43k • written 6.5 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
6.5 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
6.5 years ago manuelmendoza • 0
1
vote
6
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1.5k
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.6 years ago aec ▴ 90
0
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1
reply
1.1k
views
Interpretation of p-value plot
p values differential expression limma
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
5
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4
replies
1.4k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
0
votes
3
replies
1.0k
views
interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 90
6
votes
4
replies
1.7k
views
Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by ▴ 10
7
votes
10
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6.7k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 6.8 years ago by ▴ 30 • written 8.4 years ago by ▴ 50
7
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11
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2.9k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 60
50 results • Page 1 of 1
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Replies
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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