Showing : differential expression • reset
22
votes
17
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7.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 2.9 years ago by 41k • written 5.8 years ago by ▴ 30
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger rnaseq differential expression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 150
15
votes
12
replies
2.5k
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 5.7 years ago by 41k • written 5.7 years ago by ▴ 60
12
votes
10
replies
6.4k
views
edgeR glmLRT with test="F"?
edger dge differential expression
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ★ 7.9k
8
votes
11
replies
2.4k
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 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
7
votes
3
replies
15k
views
edgeR normalization method
edgeR differential expression normalization
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
7
votes
4
replies
4.2k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
7
votes
11
replies
2.6k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 60
7
votes
10
replies
5.7k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 6.1 years ago by ▴ 30 • written 7.8 years ago by ▴ 50
6
votes
5
replies
2.3k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.0 years ago • updated 3.9 years ago hollandademello ▴ 20
6
votes
4
replies
2.6k
views
discrepance in DESeq2 results with different design structures
deseq2 differential expression independent filtering pre-filtering design matrix
9.0 years ago Assa Yeroslaviz ★ 1.5k
6
votes
6
replies
1.8k
views
Can i set a path for readCodlinkSet()
r differential expression codelink
updated 8.9 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
6
votes
4
replies
2.3k
views
Alternate expression of splice isoforms on Affy Clariom D assay
alternate expression differential expression affy
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 20
6
votes
4
replies
1.4k
views
Fitting Gamma GLMs for examining differential expression
deseq2 edger differential expression
updated 6.1 years ago by ★ 7.9k • written 6.1 years ago by ▴ 10
5
votes
2
replies
7.2k
views
Ballgown vs (voom,edgeR,DESeq,limma)
limma rnaseq differential expression voom
updated 9.3 years ago by ▴ 210 • written 9.3 years ago by ▴ 50
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 20
5
votes
8
replies
1.8k
views
Unexpected results while analyzing a subset of genes in GEO RNAseq dataset containing TPM values
R limma TPM rnaseq differential expression
updated 4.6 years ago by ★ 13k • written 4.6 years ago by ▴ 30
5
votes
1
reply
1.2k
views
Limma - Using removeBatchEffect before differential expression analysis
limma batch effect differential expression
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
5
votes
6
replies
1.2k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by ▴ 10
5
votes
1
reply
1.0k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
5
votes
3
replies
4.0k
views
edgeR - how to convert DGELRT and other classes to .csv files
edgeR differential expression file conversion
updated 23 months ago by • 0 • written 8.2 years ago by ▴ 10
5
votes
3
replies
3.1k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 7.6 years ago by 50k • written 7.6 years ago by • 0
5
votes
4
replies
1.2k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
5
votes
4
replies
1.4k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 10
4
votes
4
replies
3.4k
views
DESeq2: Abnormally skewed distribution of p-values
deseq2 p-value distribution differential expression
8.7 years ago GFM ▴ 20
4
votes
6
replies
2.5k
views
Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger deseq2 model matrix differential expression
7.6 years ago ta65 • 0
4
votes
7
replies
1.1k
views
'NA' found under Gene Names in the list of top differentially expressed genes found using edgeR
edger differential expression TCGA Gene ID
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 60
4
votes
5
replies
3.2k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 10
4
votes
8
replies
1.9k
views
EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger glmlrt() differential expression design and contrast matrix
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
4
votes
4
replies
1.3k
views
Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
4
votes
4
replies
2.5k
views
Two-class unpaired test using LIMMA
Limma SAM differential expression
updated 9.4 years ago by 65k • written 9.4 years ago by ▴ 310
4
votes
2
replies
3.6k
views
DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
deseq2 SAMseq differential expression
updated 8.1 years ago by 41k • written 8.1 years ago by • 0
4
votes
4
replies
1.4k
views
Differential expression on codelink data
r codelink differential expression
updated 8.9 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
3
votes
4
replies
2.5k
views
How to find significantly stably expressed miRNA with DESeq2 DE results
deseq2 microrna differential expression stable expression
8.5 years ago mariakarand ▴ 20
3
votes
1
reply
1.0k
views
Obtain p-values for group * condition interaction using DESeq2?
DESeq2 interaction differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 160
3
votes
3
replies
1.5k
views
edgeR contrast formulation question
edger rnaseq differential expression
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by • 0
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.0k • written 6.3 years ago by • 0
3
votes
1
reply
1.6k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
3
votes
2
replies
1.4k
views
Moderated F-test followed by moderated t-test in limma
limma differential expression
updated 3.7 years ago by 50k • written 3.7 years ago by • 0
3
votes
5
replies
1.9k
views
DESeq2: Appropriate way to deal with knockouts in experiment design (RIPSeq)
deseq2 differential expression immunoprecipitation
updated 7.8 years ago by 41k • written 7.8 years ago by ▴ 40
3
votes
6
replies
1.2k
views
Question about edgeR usage with one case and multiple controls
edgeR differential expression without replicate
7.9 years ago gavin.oliver • 0
3
votes
10
replies
3.9k
views
Differential expression analysis of already normalized sequence counts
differential expression normalization deseq2
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 20
3
votes
5
replies
6.6k
views
Ballgown up and down regulated genes
ballgown differential expression
updated 7.0 years ago by • 0 • written 8.3 years ago by ▴ 10
3
votes
2
replies
6.2k
views
Trying to understand differential gene expression through Venn Diagrams from the 'limma' R package: why is there a number outside my diagram?
limma r venn diagram differential expression
updated 9.5 years ago by 65k • written 9.5 years ago by • 0
3
votes
1
reply
972
views
Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
3
votes
5
replies
2.1k
views
How to handle mix of samples from the same subject and from different subjects during differential expression analysis of RNA-seq using GLMs?
rnaseq rna-seq differential gene expression differential expression edger
updated 8.4 years ago by ★ 7.9k • written 8.4 years ago by ▴ 70
3
votes
4
replies
5.1k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
6.6 years ago David Requena ▴ 20
3
votes
3
replies
3.3k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
3
votes
2
replies
1.8k
views
Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 4.6 years ago by 41k • written 4.6 years ago by ▴ 10
2
votes
3
replies
2.5k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression TMM normalization rnaseq edger
7.1 years ago aec ▴ 90
50 results • Page 1 of 1
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Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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