Showing : differential expression • reset
2
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305
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Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 11 months ago by 43k • written 11 months ago by • 0
3
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3
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253
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Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 12 months ago by 33k • written 12 months ago by ▴ 20
3
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1
reply
166
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Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 12 months ago by 33k • written 12 months ago by ▴ 110
3
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5
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236
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edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
14 months ago hollandademello • 0
1
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1
reply
256
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Differential expression on Nanostring normalised protein data
R Differential expression
updated 14 months ago by 3.2k • written 14 months ago by • 0
0
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4
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273
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Agilent two-color microarray analysis with limma: 2x3 factorial design
limma microarray contrast matrix 2x3 factorial design differential expression
updated 15 months ago by 43k • written 16 months ago by • 0
2
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2
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138
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edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 15 months ago by 43k • written 15 months ago by • 0
0
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0
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116
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
16 months ago raquelponti • 0
0
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1
reply
102
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using deseq2 for intronic counts for 2 conditins with replicates
deseq2 intron differential expression
updated 16 months ago by 33k • written 16 months ago by ▴ 40
4
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7
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179
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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 16 months ago by 57k • written 16 months ago by ▴ 30
3
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4
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225
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Limma when to use zero intercept
limma regression differential expression linear model
updated 17 months ago by 43k • written 17 months ago by • 0
2
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1
reply
212
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Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
20 months ago Beginner • 0
2
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3
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331
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 20 months ago by 33k • written 20 months ago by ▴ 140
0
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1
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138
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How to handle batch effect and interaction with experimental variables
deseq2 statistics differential expression
20 months ago A • 0
0
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0
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325
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
21 months ago fawazfebin ▴ 30
6
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11
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532
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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 21 months ago by 43k • written 22 months ago by • 0
3
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6
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767
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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
22 months ago hermidalc • 0
5
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8
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395
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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 22 months ago by 13k • written 22 months ago by ▴ 30
3
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2
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315
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 22 months ago by 33k • written 22 months ago by ▴ 10
5
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6
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314
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is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 23 months ago by ▴ 750 • written 23 months ago by ▴ 10
0
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1
reply
272
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
23 months ago Andrew_McDavid ▴ 260
17
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17
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2.8k
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DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 8 weeks ago by 33k • written 3.1 years ago by ▴ 20
2
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4
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295
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Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 2.1 years ago by ★ 27k • written 2.1 years ago by • 0
1
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1
reply
271
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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 2.1 years ago by 33k • written 2.1 years ago by ▴ 30
4
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4
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273
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 2.1 years ago by 33k • written 2.1 years ago by ▴ 30
1
vote
12
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402
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 70
4
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5
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414
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How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
1
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1
reply
287
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How to normalize RNA-seq when 50% genes are DE? (TMM)
limma TMM differential expression normalization rnaseq
updated 2.3 years ago by 57k • written 2.3 years ago by • 0
0
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1
reply
403
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
2.4 years ago baldissera152 • 0
5
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1
reply
350
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Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 2.4 years ago by 57k • written 2.4 years ago by • 0
0
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2
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706
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.5 years ago by 25k • written 2.5 years ago by ▴ 30
0
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3
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515
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How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
1
vote
1
reply
414
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
2.6 years ago krassowski.michal ▴ 10
2
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7
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772
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Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
15
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12
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1.2k
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 3.0 years ago by 33k • written 3.0 years ago by ▴ 60
1
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3
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568
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Global expression shift using RUVSeq
ruvseq rnaseq normalization differential expression
updated 3.0 years ago by ▴ 870 • written 3.1 years ago by • 0
1
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4
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572
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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 3.1 years ago by 57k • written 3.1 years ago by ▴ 40
5
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1
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435
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 3.1 years ago by ★ 27k • written 3.1 years ago by • 0
0
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4
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642
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Deseq2 problem visualizing gene expression with batch corrected values
deseq2 limma differential expression visualization
updated 3.1 years ago by 33k • written 3.1 years ago by • 0
1
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4
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500
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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 3.1 years ago by 33k • written 3.1 years ago by ▴ 20
0
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0
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370
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pair wise ballgown
ballgown differential expression
3.1 years ago zoe.ward • 0
0
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0
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447
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Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential gene expression differential expression
3.1 years ago manuelmendoza • 0
1
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6
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521
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
3.2 years ago aec ▴ 70
0
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1
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431
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Interpretation of p-value plot
p values differential expression limma
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
5
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4
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476
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Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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3
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400
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interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 3.3 years ago by 33k • written 3.3 years ago by ▴ 70
6
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4
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518
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Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 3.4 years ago by 7.6k • written 3.4 years ago by ▴ 10
4
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10
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2.6k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 3.4 years ago by ▴ 10 • written 5.0 years ago by ▴ 30
7
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11
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1.2k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 30
1
vote
4
replies
996
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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Comment: An error using Diffbind plotprofile by doug.barrows • 0
Hi there, it's hard to tell how to debug without having the data. Could you potentially send me the object you are attempting to use for th…
Comment: DESeq2 Shrinkage methods for scRNA-Seq by Pedro Tan • 0
Thanks Michael! I will stick to apeglm and incorporate alternate size factors for single cell data. All the best, Pedro
Answer: Macbook M1 install genefilter failed by soda ▴ 10
i have solved this problem by myself. share with you. you need to download gfortran in path /opt/R/arm64/bin this website helped me: **h…
Comment: Best practice for quantifying sncRNA by James W. MacDonald 57k
If you used the QIASeq miRNA library, then you are wasting your time. That library adds the UMI barcodes and is intended for you to then up…
Answer: BioCAsia Virtual Meeting, 15-18 October 2020 by Cassandra Holmes • 0
All the types of bio-conductors are presented to the buyers. The change of the [proposal writing help][1] is ensured for the users. The bio…
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Answer: Macbook M1 install genefilter failed
BioCAsia Virtual Meeting, 15-18 October 2020
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
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