Showing : differential expression • reset
3
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4
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Protein differential Expression analysis
differential expression proteomics
updated 19 months ago by ★ 4.8k • written 7.3 years ago by • 0
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 7.5 years ago by • 0
3
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3
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4.3k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.1 years ago by ▴ 30 • written 6.2 years ago by ▴ 40
4
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2
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2.1k
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 4.6 years ago by 52k • written 4.6 years ago by • 0
5
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3
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1.9k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 20
3
votes
1
reply
1.4k
views
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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3.4k
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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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2.1k
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 4.9 years ago by ★ 4.0k • written 4.9 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 5.0 years ago by • 0
2
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2
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940
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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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922
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
5.0 years ago raquelponti • 0
0
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1
reply
885
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 40
4
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7
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1.6k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 60
7
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4
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6.3k
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Limma when to use zero intercept
limma regression differential expression linear model
updated 5.1 years ago by 52k • written 5.1 years ago by • 0
2
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1
reply
809
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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
reply
1.1k
views
How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
5.4 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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3.2k
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 5.5 years ago by 52k • written 5.5 years ago by ▴ 20
5
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8
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2.3k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 5.5 years ago by ★ 13k • written 5.5 years ago by ▴ 30
3
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2
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2.4k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 5.5 years ago by 43k • written 5.6 years ago by ▴ 10
5
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6
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1.7k
views
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
reply
2.3k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.6 years ago Andrew_McDavid ▴ 280
27
votes
17
replies
9.0k
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
2
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4
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1.7k
views
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
reply
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 5.8 years ago by 43k • written 5.8 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 5.8 years ago by 43k • written 5.8 years ago by ▴ 40
1
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12
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1.8k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 90
4
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5
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5.5k
views
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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1.5k
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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
views
How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by • 0
1
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1
reply
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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2.7k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
15
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12
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3.1k
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 6.6 years ago by 43k • written 6.6 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 6.7 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
0
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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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1.5k
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
6.8 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
6.9 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 6.9 years ago by 52k • written 6.9 years ago by • 0
5
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4
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1.5k
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Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.9 years ago by 52k • written 7.0 years ago by • 0
0
votes
3
replies
1.1k
views
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
votes
4
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1.8k
views
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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7.1k
views
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
views
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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Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR by Gordon Smyth 52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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