Showing : edgeR • reset
0
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624
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Error message when trying to access packages
edger software error bioconductor
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
4
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15
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2.7k
views
Adjusting for procedural effect and deciding on statistical test
EdgeR glmlrt() ql f-test
9.1 years ago • updated 8.4 years ago elineverbon ▴ 20
0
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1
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931
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bug in kegga() when using prior.prob?
limma edgeR
updated 8.4 years ago by 53k • written 8.4 years ago by ★ 2.0k
1
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2
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1.8k
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accounting for phylogenetic non-independence in differential expression analysis
edger differential expression phylogenetic comparative methods
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 10
2
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4
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4.2k
views
Filtering DGEList object in edgeR
DGElist filter edgeR
updated 8.4 years ago by 53k • written 8.4 years ago by ▴ 130
5
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4
replies
2.8k
views
Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma
edgeR deseq2 chipseq limma
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 120
2
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2
replies
695
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using edgeR or limma for 5C data normalization
limma edgeR deseq2
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 670
0
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1
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1.5k
views
EdgeR dispersion and FDR
edger FDR rnaseq
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
0
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3
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1.8k
views
kegga() p-value calculated differently in different edgeR versions
edger kegga
updated 8.4 years ago by 53k • written 8.4 years ago by • 0
2
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2
replies
2.7k
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EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
0
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2
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1.5k
views
CRISPR/RNAi screen time course analysis
edger high-throughput screening
8.4 years ago knaxerova ▴ 10
2
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1
reply
1.7k
views
Decide normalisation method in RUVseq for RNAseq data
edger ruvseq rnaseq normalization ruvnormalize
updated 8.4 years ago by ▴ 980 • written 8.4 years ago by • 0
6
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4
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7.2k
views
RNAseq with technical replicates: Does it sound right?
rnaseq edger technical replicates
updated 8.4 years ago by ★ 7.9k • written 8.4 years ago by ▴ 130
1
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1
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4.6k
views
edgeR reinstall failure: edgeR.rdb' is corrupt
edgeR package installation
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
1
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3
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1.3k
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edgeR 4 conditions
edger
8.4 years ago Paolo Kunderfranco ▴ 350
4
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3
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3.1k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger deseq deseq2
8.4 years ago michael.steffen ▴ 20
2
votes
5
replies
4.3k
views
Trouble with DESeq2, edgeR, and limma not accepting zeros in input
limma deseq2 edgeR
updated 8.5 years ago by 53k • written 8.5 years ago by • 0
0
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4
replies
2.1k
views
setting contrast in edgeR for time series data
rnaseq edger makecontrasts
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
1
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1
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1.8k
views
older version of edger installation
edger
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
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1
reply
676
views
egeR GLM approach
edger
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
2
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2
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1.5k
views
miRNA differential expression analysis
edger glm.fit
updated 8.5 years ago by 53k • written 8.5 years ago by • 0
1
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3
replies
2.6k
views
edgeR multiple coeff in "lrt <- glmLRT(fit, coef=)"
edger
8.5 years ago zhang.jianhai ▴ 10
0
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7
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1.4k
views
Design matrix and contrast formation in edgeR for DE analysis
edger
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
0
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5
replies
2.8k
views
normalization factors for ChIP/RNA-IP-seq data
edgeR DESeq edgeR DESeq
updated 8.5 years ago by • 0 • written 13.9 years ago by ▴ 370
0
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3
replies
2.1k
views
Using Combat function of SVA to remove known batch effect and using the result for down-stream analysis
sva batch effect deseq2 edgeR
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 10
5
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4
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1.8k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 8.5 years ago by • 0 • written 8.5 years ago by ▴ 40
4
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2
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2.2k
views
Help: extract counts from RNA-seq .bam/.bai files
counts edger
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 80
1
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3
replies
2.1k
views
Three factor model matrix, contrasts with interactions - DESeq2 / edgeR
deseq2 edgeR multifactorial design limma voom
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 150
5
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4
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1.9k
views
interpretation of edgeR multi factor conditions in GLM
edger multivariate multiple factor design glm
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by • 0
6
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4
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3.8k
views
Can edgeR TMM normalization be used for other count data?
edgeR tmm normalization counts
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 40
3
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3
replies
1.6k
views
Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tests
limma edgeR sva RNA-Seq
updated 8.6 years ago by 53k • written 8.6 years ago by • 0
1
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1
reply
1.7k
views
edgeR p.adjust FDR = 0?
edger adjusted pvalue
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
votes
1
reply
872
views
arrayExpress differential gene express analysis
deseq2 limma bioconductor edger microarray
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
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2
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1.4k
views
Diffbind: getting the raw reads
edger diffbind raw reads
8.6 years ago veronique.storme • 0
6
votes
5
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5.0k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 8.6 years ago by 53k • written 8.6 years ago by ▴ 20
2
votes
2
replies
2.8k
views
Pairwise differential expression analysis with batch effect using edgeR and SVA
edger rna-seq sva differential expression
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
0
votes
7
replies
4.3k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
8.6 years ago Jeff Skinner • 0
2
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3
replies
3.2k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression TMM normalization rnaseq edger
8.6 years ago aec ▴ 90
1
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1
reply
3.3k
views
EdgeR 'average' cpm
edgeR
updated 8.6 years ago by 53k • written 12.6 years ago by ▴ 20
4
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3
replies
5.0k
views
EdgeR on miRNA data
edger miRNA
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
3
votes
3
replies
1.3k
views
[edgeR Usage] Constructing DGE test with fewer input variables
edger
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 10
1
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2
replies
1.4k
views
How to transform edgeR output into a cummeRbund object?
edgeR cummeRbund
8.7 years ago alakatos ▴ 130
12
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6
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3.3k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger differential gene expression rnaseq
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 20
2
votes
6
replies
1.9k
views
How to do multivariate glmFit analysis of RNA-seq with edgeR
limma edger rnaseq
8.7 years ago mousheng xu ▴ 10
6
votes
4
replies
5.8k
views
Is there any point to TMM-normalize TPM prior to limma-voom?
voom limma-voom tximport edger
updated 8.7 years ago by ★ 7.9k • written 8.7 years ago by ▴ 10
5
votes
7
replies
12k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 22 months ago by • 0 • written 8.7 years ago by • 0
2
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1
reply
1.7k
views
Adjusting p-values from goana() output
edger limma
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
4
votes
6
replies
3.8k
views
Timecourse Differential expression with multiple factors
deseq2 edger timecourse
8.7 years ago anna_stavrinides ▴ 20
4
votes
3
replies
1.7k
views
plotMDS Input Feature Filtering
edgeR Exploratory Data Analysis
updated 8.7 years ago by 53k • written 8.7 years ago by ★ 1.6k
2
votes
3
replies
2.6k
views
edgeR ANOVA-like analysis
edger rnaseq anova
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
2,031 results • Page 20 of 41
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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