Showing : edgeR • reset
2
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2
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9.4k
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edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
9.0 years ago jol.espinoz ▴ 40
4
votes
4
replies
15k
views
Filtering read counts matrix: how to deal with duplicated gene symbols, different ENSEMBL ids
edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 20
1
vote
4
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1.1k
views
EdgeR multiple factor design question
edger design matrix
9.0 years ago bioinformatics ▴ 30
1
vote
1
reply
770
views
EdgeR two condition problem
edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 30
1
vote
3
replies
1.2k
views
readDGE function does not exist
edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 160
2
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4
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5.7k
views
Error in estimateGLMCommonDisp and glmFit
edger
9.0 years ago andrluis • 0
9
votes
9
replies
3.2k
views
edgeR: Tagwise dispersion when using offset matrix
edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 10
0
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1
reply
1.2k
views
ISO help making a colored pathway diagram to display enriched KEGG pathways
limma edger
updated 9.0 years ago by 53k • written 9.0 years ago by ▴ 80
4
votes
9
replies
2.1k
views
RNA-seq analysis edgeR
rna-seq edger
updated 9.0 years ago by ★ 7.9k • written 9.0 years ago by ▴ 20
0
votes
2
replies
1.3k
views
can a batch effect be determined in edgeR with only 2 reps?
edger rnaseq batch effect read length
9.0 years ago Spollen, William G. ▴ 30
0
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1
reply
2.1k
views
edgeR estimateGLMRobustDisp fails with and error
rnaseq edger
updated 9.0 years ago by ★ 29k • written 9.0 years ago by ▴ 750
1
vote
6
replies
1.9k
views
edgeR time series DMSO correction
edger makecontrasts timecourse
updated 9.0 years ago by ★ 7.9k • written 9.0 years ago by ▴ 90
3
votes
7
replies
2.0k
views
edgeR RNA-seq analysis using glm
edger rna-seq
updated 9.0 years ago by ★ 7.9k • written 9.0 years ago by ▴ 20
0
votes
6
replies
4.6k
views
Unable to load edgeR with bioconductor
edger
updated 9.1 years ago by ▴ 130 • written 9.1 years ago by • 0
0
votes
2
replies
1.5k
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 10
2
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3
replies
3.7k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
1
vote
2
replies
1.4k
views
2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in others
rnaseq edger differential expression dispersion
updated 9.1 years ago by ★ 7.9k • written 9.1 years ago by • 0
3
votes
2
replies
8.0k
views
Non-integer counts from tximport OK for edgeR / DESeq2?
tximport edgeR DESeq2
updated 9.1 years ago by 43k • written 9.1 years ago by ★ 2.0k
1
vote
3
replies
2.8k
views
How to combine replicates creating heatmap?
deseq2 edgeR heatmap.2
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 50
2
votes
3
replies
3.2k
views
edgeR with unequal no.of replicate
edgeR replicate
updated 9.1 years ago by • 0 • written 9.9 years ago by • 0
3
votes
3
replies
1.5k
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
9.1 years ago jjh • 0
4
votes
2
replies
3.0k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 20
4
votes
13
replies
3.6k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2 EDGER design
9.1 years ago ZheFrench ▴ 60
1
vote
5
replies
1.4k
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
9.1 years ago sezimmer • 0
1
vote
5
replies
2.3k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
0
votes
3
replies
1.9k
views
How to remove nested batch effects with removeBatchEffect?
edgeR removeBatchEffect nested design
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ★ 2.0k
1
vote
10
replies
2.9k
views
edgeR: AveLogCPM after estimateGLMCommonDisp
rnaseq edger
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 90
5
votes
5
replies
3.7k
views
Why the log fold change of some genes returned by edgeR is not compatible with their related FPKM value?
edgeR logFC FPKM
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 20
3
votes
4
replies
1.2k
views
EdgeR, between/within subject comparisons
edger
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 10
5
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4
replies
4.3k
views
Normalization factor in TMM method
TMM normalization edgeR
updated 9.1 years ago by 68k • written 9.1 years ago by ▴ 20
3
votes
3
replies
3.3k
views
[EdgeR] question about the y$samples$lib.size and y$samples$norm.factors
edger
9.2 years ago • updated 9.1 years ago wbli2012 • 0
0
votes
1
reply
896
views
about sets of replicates in RNA-seq and quality controls
rnaseq limma edgeR deseq2
updated 9.1 years ago by ★ 3.8k • written 9.1 years ago by ▴ 670
3
votes
3
replies
6.1k
views
edgeR and removeBatchEffect()
edger limma
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 670
1
vote
2
replies
1.1k
views
EdgeR GLM, when factor categories are not equaly represented in different groups
edger
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 140
4
votes
4
replies
1.5k
views
how to export data as excel file from plotSmear when using edgeR
edger
updated 9.2 years ago by 53k • written 9.2 years ago by • 0
3
votes
14
replies
3.6k
views
limma-voom or edgeR for paired designs both within and between comparisons
edger limma-voom paired samples
9.2 years ago aec ▴ 90
2
votes
13
replies
2.2k
views
How to account for population variation within regions in EdgeR?
edger multifactor nested design
9.3 years ago • updated 9.2 years ago swaegers.janne • 0
1
vote
1
reply
1.4k
views
edgeR: Nested interactions model matrix MISSING COEFFICIENTS
limma edger nested design
updated 9.2 years ago by ★ 7.9k • written 9.2 years ago by • 0
4
votes
4
replies
1.9k
views
Correlation analysis taking into account multiple correlations
edger rna-seq correlation
updated 9.2 years ago by ▴ 280 • written 9.2 years ago by ▴ 10
3
votes
1
reply
2.0k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 9.2 years ago by ★ 29k • written 9.2 years ago by • 0
4
votes
6
replies
3.1k
views
Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger deseq2 model matrix differential expression
9.2 years ago ta65 • 0
3
votes
6
replies
6.7k
views
RNAseq, what to do if you have no replicates in voom-limma
limma voom edger
updated 9.2 years ago by ▴ 20 • written 10.4 years ago by ▴ 80
4
votes
3
replies
1.8k
views
including information indicating upregulation/downregulation of genes in goana()
edger goana
updated 9.2 years ago by 68k • written 9.2 years ago by ▴ 10
5
votes
3
replies
3.8k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 9.2 years ago by 53k • written 9.2 years ago by • 0
3
votes
6
replies
3.2k
views
EdgeR glmLRT vs glmQL - hundreds of DE genes with glmLRT, almost none with glmQL
edgeR
9.2 years ago miyakokodama • 0
3
votes
2
replies
1.6k
views
ROAST after edgeR glmTreat and average RPKM filter
roast edgeR glmtreat
updated 9.2 years ago by ★ 29k • written 9.2 years ago by ▴ 370
1
vote
2
replies
2.5k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger filtering cpm
updated 9.2 years ago by 53k • written 9.2 years ago by • 0
0
votes
2
replies
1.4k
views
how to incorporate count bias in Goseq
goseq edgeR
updated 9.2 years ago by ▴ 10 • written 9.2 years ago by ▴ 140
8
votes
8
replies
5.0k
views
Disagreement between TMM (edgeR) and RLE (DESeq) normalisation for single-cell data
rnaseq single cell normalization edgeR deseq2
updated 9.2 years ago by ★ 29k • written 9.2 years ago by ▴ 50
4
votes
4
replies
3.2k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 9.2 years ago by ★ 29k • written 9.2 years ago by • 0
2,031 results • Page 22 of 41
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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 …
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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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