Showing : differential expression • reset
22
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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
0
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17
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3.4k
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What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
15
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12
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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
1
vote
12
replies
1.4k
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RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 90
7
votes
11
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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
8
votes
11
replies
2.3k
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
12
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10
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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
3
votes
10
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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
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
2
votes
9
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2.3k
views
Limma: Defining the design matrix of a linear mixed model
rnaseq limma differential expression
7.3 years ago • updated 7.2 years ago j.baldauf • 0
5
votes
8
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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
4
votes
8
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1.9k
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EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger glmlrt() differential expression design and contrast matrix
updated 8.8 years ago by 50k • written 8.9 years ago by • 0
2
votes
8
replies
2.5k
views
Limma for differential expression in a time-course
limma multiple time points time-course differential expression
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
2
votes
8
replies
1.3k
views
Deseq2 result for a variable
deseq2 differential expression results
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
2
votes
7
replies
2.1k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.7 years ago by 50k • written 5.7 years ago by • 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
0
votes
6
replies
3.9k
views
Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :
R differential expression rnaseqgene
8.5 years ago JunLVI ▴ 40
1
vote
6
replies
1.3k
views
differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
6.0 years ago aec ▴ 90
4
votes
6
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2.5k
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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
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
1
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6
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3.4k
views
Two-way anova 2x2 design with limma
limma microarray differential expression
6.5 years ago • updated 6.4 years ago damoros • 0
6
votes
6
replies
1.8k
views
Can i set a path for readCodlinkSet()
r differential expression codelink
updated 8.8 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
5
votes
6
replies
1.2k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.6 years ago by ▴ 840 • written 4.7 years ago by ▴ 10
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
2
votes
5
replies
1.2k
views
Comparing across sets of regulated genes -- Strategies?
limma differential expression
updated 7.2 years ago by ▴ 730 • written 7.2 years ago by ▴ 30
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
1
vote
5
replies
997
views
differential expression analysis in edgeR when you have 2 experiments and batch effect in 1 of the 2 experiments.
edger batch effect differential expression
7.5 years ago sezimmer • 0
1
vote
5
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7.4k
views
DESeq2 and edgeR getting very different results
edger deseq2 differential expression
updated 6.4 years ago by ▴ 20 • written 6.4 years ago by • 0
2
votes
5
replies
1.7k
views
Codelink differential expression and annotation
r codelink differential expression hwgcod
updated 8.9 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
6
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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
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
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
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
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
1
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4
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1.2k
views
Specifically expressed genes
DESeq2 specific expression rnaseq clustering differential expression
updated 9.0 years ago by 41k • written 9.0 years ago by • 0
4
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4
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3.4k
views
DESeq2: Abnormally skewed distribution of p-values
deseq2 p-value distribution differential expression
8.7 years ago GFM ▴ 20
6
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4
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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
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
1
vote
4
replies
2.2k
views
How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
2
votes
4
replies
1.3k
views
Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 4.8 years ago by ★ 28k • written 4.8 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
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
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
1
vote
4
replies
1.2k
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 5.8 years ago by 41k • written 5.8 years ago by ▴ 50
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
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
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
1
vote
4
replies
1.2k
views
How to return probelist,FC and p-value column by putting a p-value threshold in Limma
r limma differential expression
updated 8.9 years ago by 50k • written 8.9 years ago by ▴ 260
2
votes
4
replies
8.5k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma differential expression design matrix error eset
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
6
votes
4
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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
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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