Showing : differential expression • reset
2
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220
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 8 months ago by 42k • written 8 months ago by • 0
3
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3
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194
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Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 9 months ago by 32k • written 9 months ago by • 0
3
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1
reply
130
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Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 10 months ago by 32k • written 10 months ago by ▴ 100
3
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5
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176
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
11 months ago hollandademello • 0
1
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1
reply
155
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 12 months ago by 2.9k • written 12 months ago by • 0
0
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4
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223
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 12 months ago by 42k • written 13 months ago by • 0
2
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2
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100
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 13 months ago by 42k • written 13 months ago by • 0
0
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0
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80
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
13 months ago raquelponti • 0
0
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1
reply
79
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 13 months ago by 32k • written 13 months ago by ▴ 40
4
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7
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120
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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 13 months ago by 56k • written 13 months ago by ▴ 30
3
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4
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159
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Limma when to use zero intercept
limma regression differential expression linear model
updated 14 months ago by 42k • written 14 months ago by • 0
2
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1
reply
178
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Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
18 months ago • updated 17 months ago Beginner • 0
2
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3
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248
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 17 months ago by 32k • written 17 months ago by ▴ 130
0
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1
reply
113
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
18 months ago A • 0
0
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0
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276
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
18 months ago fawazfebin ▴ 30
6
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11
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389
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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 19 months ago by 42k • written 19 months ago by • 0
3
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6
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608
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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
19 months ago hermidalc • 0
5
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8
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311
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 19 months ago by 13k • written 19 months ago by ▴ 30
3
votes
2
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220
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 19 months ago by 32k • written 19 months ago by ▴ 10
5
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6
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252
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is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 20 months ago by ▴ 720 • written 20 months ago by ▴ 10
0
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1
reply
209
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
20 months ago Andrew_McDavid ▴ 260
16
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11
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2.4k
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 22 months ago by • 0 • written 2.9 years ago by ▴ 20
2
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4
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242
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Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 22 months ago by ★ 26k • written 22 months ago by • 0
1
vote
1
reply
230
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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 23 months ago by 32k • written 23 months ago by ▴ 20
4
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4
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232
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 23 months ago by 32k • written 23 months ago by ▴ 20
1
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12
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333
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 23 months ago by 42k • written 23 months ago by ▴ 70
3
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5
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304
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How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 23 months ago by 42k • written 23 months ago by • 0
1
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1
reply
253
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 2.1 years ago by 56k • written 2.1 years ago by • 0
0
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1
reply
311
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
2.2 years ago baldissera152 • 0
5
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1
reply
309
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Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 2.2 years ago by 56k • written 2.2 years ago by • 0
0
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2
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578
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.3 years ago by 25k • written 2.3 years ago by ▴ 30
0
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3
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466
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 2.3 years ago by • 0 • written 2.3 years ago by • 0
1
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1
reply
350
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
2.3 years ago krassowski.michal ▴ 10
2
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7
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700
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Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
15
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12
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1.1k
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 2.7 years ago by 32k • written 2.7 years ago by ▴ 60
1
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3
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503
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 2.8 years ago by ▴ 870 • written 2.8 years ago by • 0
1
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4
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470
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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 2.8 years ago by 56k • written 2.8 years ago by ▴ 40
5
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1
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397
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 2.8 years ago by ★ 26k • written 2.8 years ago by • 0
0
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4
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582
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 2.9 years ago by 32k • written 2.9 years ago by • 0
1
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4
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455
views
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 2.9 years ago by 32k • written 2.9 years ago by ▴ 20
0
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0
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333
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pair wise ballgown
ballgown differential expression
2.9 years ago zoe.ward • 0
0
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0
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408
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
2.9 years ago manuelmendoza • 0
1
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6
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473
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
3.0 years ago aec ▴ 70
0
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1
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405
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Interpretation of p-value plot
p values differential expression limma
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
5
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4
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434
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Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
0
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3
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363
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interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 3.1 years ago by 32k • written 3.1 years ago by ▴ 70
6
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4
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474
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Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 3.1 years ago by 7.6k • written 3.1 years ago by ▴ 10
4
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10
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2.4k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 3.2 years ago by ▴ 10 • written 4.8 years ago by ▴ 30
7
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11
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1.1k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 3.2 years ago by 42k • written 3.2 years ago by ▴ 30
1
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4
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897
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
132 results • Page 1 of 3
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Comment: Need help in running GO analysis by Rishav ▴ 10
Yes, I already solved that problem. I understand what was the problem . Thank you so much for your time
Answer: DESeq2 ashr with and without reflevels generate different log2FoldChanges by Michael Love 32k
*"How is it possible to get different log2FC using lfcShrink (ashr) by defining relevels compared to no relevels defining?"* This has be…
Comment: After having the output from SingleR for cell type annotation, what's the next s by sofiagreen72211 ▴ 10
I believe, you have a seurat object with 3 groups with barcodes. If this is the case, it's straight forward, get singleR predictions on eac…
Comment: Cannot install packages by BiocManager::install() by FairerBadge66 • 0
Thank you very much, it works, I was loosing my mind already.
Comment: Affymetrix miRNA 4.0 Normalization and Analysis by S • 0
Hello, Before applying limma it is recommended to remove low expressed probes. I am not sure about how to perform this filtering step based…
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Answer: Need help in running GO analysis
Answer: how can I annotate my scRNAseq clusters from a Rat experiment?
Answer: how can I annotate my scRNAseq clusters from a Rat experiment?
Comment: Cannot install packages by BiocManager::install()
Comment: Unable to install packages on MacOS
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