Showing : differential expression • reset
2
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454
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 17 months ago by 44k • written 17 months ago by • 0
3
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3
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360
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Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 18 months ago by 35k • written 18 months ago by ▴ 20
3
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1
reply
279
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Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 18 months ago by 35k • written 18 months ago by ▴ 110
3
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5
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401
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
20 months ago hollandademello • 0
1
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1
reply
414
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 20 months ago by 3.4k • written 20 months ago by • 0
0
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4
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392
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 21 months ago by 44k • written 22 months ago by • 0
2
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2
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218
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 21 months ago by 44k • written 21 months ago by • 0
0
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0
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197
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
21 months ago raquelponti • 0
0
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1
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165
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 21 months ago by 35k • written 21 months ago by ▴ 40
4
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7
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290
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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 22 months ago by 58k • written 22 months ago by ▴ 30
3
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4
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512
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Limma when to use zero intercept
limma regression differential expression linear model
updated 23 months ago by 44k • written 23 months ago by • 0
2
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1
reply
280
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Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
2.2 years ago • updated 2.1 years ago Beginner • 0
2
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3
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500
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 2.2 years ago by 35k • written 2.2 years ago by ▴ 150
0
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1
reply
195
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
2.2 years ago A • 0
0
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0
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450
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
2.2 years ago fawazfebin ▴ 30
7
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11
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814
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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 2.3 years ago by 44k • written 2.3 years ago by ▴ 10
3
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6
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1.0k
views
Multiple samples per individual and unbalanced number of samples per individual: DE between groups still an ordinary two-group comparison?
limma edger deseq2 differential expression repeated measures
2.3 years ago hermidalc ▴ 10
5
votes
8
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585
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 2.3 years ago by 13k • written 2.3 years ago by ▴ 30
3
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2
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475
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 2.3 years ago by 35k • written 2.3 years ago by ▴ 10
5
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6
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464
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is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 2.4 years ago by ▴ 770 • written 2.4 years ago by ▴ 10
0
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1
reply
422
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
2.4 years ago Andrew_McDavid ▴ 260
17
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17
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3.5k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 7 months ago by 35k • written 3.6 years ago by ▴ 20
2
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4
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371
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Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 2.6 years ago by ★ 27k • written 2.6 years ago by • 0
1
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1
reply
379
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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 2.6 years ago by 35k • written 2.6 years ago by ▴ 30
4
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4
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447
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 2.6 years ago by 35k • written 2.6 years ago by ▴ 30
1
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12
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514
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 2.6 years ago by 44k • written 2.6 years ago by ▴ 70
4
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5
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707
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 2.7 years ago by 44k • written 2.7 years ago by ▴ 10
1
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1
reply
348
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
0
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1
reply
540
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
2.8 years ago baldissera152 • 0
5
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1
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433
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Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 2.9 years ago by 58k • written 2.9 years ago by • 0
0
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2
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958
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.0 years ago by 25k • written 3.0 years ago by ▴ 30
0
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3
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667
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by • 0
1
vote
1
reply
521
views
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
3.0 years ago krassowski.michal ▴ 10
2
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7
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905
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Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 3.4 years ago by 44k • written 3.4 years ago by • 0
15
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12
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1.5k
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 3.4 years ago by 35k • written 3.4 years ago by ▴ 60
1
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3
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716
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 3.5 years ago by ▴ 870 • written 3.5 years ago by • 0
1
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4
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674
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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 3.5 years ago by 58k • written 3.5 years ago by ▴ 40
5
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1
reply
506
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 3.5 years ago by ★ 27k • written 3.5 years ago by • 0
0
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4
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747
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 3.6 years ago by 35k • written 3.6 years ago by • 0
1
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4
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578
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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 3.6 years ago by 35k • written 3.6 years ago by ▴ 50
0
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0
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427
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pair wise ballgown
ballgown differential expression
3.6 years ago zoe.ward • 0
0
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0
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537
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
3.6 years ago manuelmendoza • 0
1
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6
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608
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
3.7 years ago aec ▴ 70
0
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1
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482
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Interpretation of p-value plot
p values differential expression limma
updated 3.7 years ago by 44k • written 3.7 years ago by • 0
5
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4
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560
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Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 3.7 years ago by 44k • written 3.7 years ago by • 0
0
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3
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456
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interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 3.7 years ago by 35k • written 3.7 years ago by ▴ 70
6
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4
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625
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Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 3.8 years ago by 7.7k • written 3.8 years ago by ▴ 10
7
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10
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3.0k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 3.8 years ago by ▴ 10 • written 5.5 years ago by ▴ 50
7
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11
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1.4k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 3.9 years ago by 44k • written 3.9 years ago by ▴ 30
1
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4
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1.1k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 3.9 years ago by 44k • written 3.9 years ago by • 0
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Comment: Cannot install Phyloseq and dada2 by Guido Hooiveld ★ 3.2k
Did you notice this message:? Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.0.0/libra…
Comment: Use of shrunken LFCs to address questions about the distribution of LFCs between by i.sudbery ▴ 20
Thanks Mike. I might have a play with stratifying by expression level. One reason I wasn't looking at gene set testing is that its the nul…
Answer: submitting a BSgenome package by deisianyufg • 0
From my Github repository. I am sorry, I thought the package was already released and realize now that is still only in my github reposito…
Comment: PlotPCA in DESeq2 doesn't produce exactly the same result as prcomp by swbarnes2 ▴ 970
Is the one plot a mirror image of the other?
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between by Michael Love 35k
hi Ian, Great question, and good to be concerned that the mean expression may be a confounder for either analysis, Why not stratify your…
Votes
Answer: Use of shrunken LFCs to address questions about the distribution of LFCs between
Answer: DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
Comment: submitting a BSgenome package
Answer: rlog vs vst for outlier identification
Answer: DESeq2 median of ratios normalization for signature score calculation
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