Showing : EDGER • reset
3
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3
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1.2k
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edgeR: the F-statistics changed after removing lowly expressed gene
glmQLFTest edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
1
vote
1
reply
710
views
could edgeR be applied to gene counts by gene family to make group comparisons?
edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
votes
6
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2.0k
views
Variance explained (coefficient of determination) in edgeR
edgeR
3.5 years ago Gemma • 0
2
votes
2
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1.6k
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
3.5 years ago Sarah • 0
0
votes
2
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1.2k
views
Variance explained (coefficient of determination) in glmFit / glmLRT
edgeR
3.5 years ago Gemma • 0
0
votes
1
reply
1.7k
views
How to directly decet the outlier samples (libraries) in EdgeR pipeline
edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 30
5
votes
14
replies
7.4k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.5 years ago by ★ 5.0k • written 7.3 years ago by ▴ 60
0
votes
0
replies
774
views
diffcyt - topTable function returns one total significance estimate instead of one per comparison
limma diffcyt edgeR
3.5 years ago stefanos.bamopoulos • 0
1
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1
reply
1.3k
views
Should I keep libsizes?
Normalization edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
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7
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2.0k
views
edgeR: topTags weird behavior - outputting NAs
edgeR
3.5 years ago venura • 0
0
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2
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1.5k
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edgeR: Analyzing multiple factors with batch effects
edgeR
3.5 years ago venura • 0
0
votes
11
replies
3.2k
views
EdgeR function nearestTSS() fails with org.Ss.eg.db
Sus_scrofa edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
4
replies
1.5k
views
Extremely different results for both EdgeR and DESeq2 analysis
edgeR DESeq2
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
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5
replies
1.5k
views
edgeR: Combining time series analysis with mock and treated samples
edgeR
3.5 years ago venura • 0
0
votes
2
replies
995
views
edgeR
rnaseq edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
11
replies
2.4k
views
Differential methilation analysis - Design matrix not of full rank
DifferentialMethylation RRBSdata edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
5
votes
6
replies
4.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
3.5 years ago Alan • 0
0
votes
1
reply
1.8k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.5 years ago by 53k • written 3.6 years ago by • 0
2
votes
4
replies
1.2k
views
I want to clarify difference between below two codes for analysis of DEGs. I got two different answers with these two methods and would like to know …
edgeR
3.6 years ago devi • 0
0
votes
1
reply
1.3k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
2
replies
2.9k
views
RNA-seq: problems with edgeR installation
BiocManager edgeR
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
votes
17
replies
3.2k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 3.6 years ago by • 0
0
votes
0
replies
827
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
3.6 years ago Mafalda • 0
0
votes
1
reply
6.5k
views
Why does my volcano plot look weird?
edgeR volcano_plot
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
2
votes
3
replies
1.4k
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
0
votes
0
replies
4.2k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.6 years ago Raito92 ▴ 60
15
votes
18
replies
5.1k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 60
2
votes
1
reply
1.1k
views
How to determine which model (GLM and QLF or classic edgeR) to use for DGE analysis?
edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
0
votes
1
reply
2.8k
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
6
votes
2
replies
957
views
The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 30
1
vote
2
replies
2.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
1
vote
2
replies
1.9k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.7 years ago Adelyn ▴ 10
2
votes
5
replies
1.9k
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
1
reply
1.2k
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
3
votes
6
replies
2.6k
views
filterbyexp() in edgeR
edgeR
updated 13 months ago by ▴ 900 • written 3.7 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.7 years ago Raito92 ▴ 60
0
votes
6
replies
5.3k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 60
2
votes
3
replies
6.1k
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 3.5 years ago by • 0 • written 3.8 years ago by • 0
1
vote
4
replies
2.2k
views
Differential Splicing using edgeR
diffSpliceDGE edgeR DifferentialSplicing
3.8 years ago Assa Yeroslaviz ★ 1.5k
0
votes
3
replies
2.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.8 years ago by 53k • written 3.8 years ago by ▴ 90
3
votes
6
replies
3.2k
views
How to use subjunc for differential splicing analysis?
subjunc edgeR
3.8 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.3k
views
catchKallisto results are not counts
DifferentialSplicingWorkflow catchKallisto edgeR DifferentialSplicing
3.8 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
1.4k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
0
votes
5
replies
1.4k
views
ANOVA-like vs direct contrast
edgeR
3.8 years ago fcamus • 0
2
votes
2
replies
5.1k
views
EdgeR installation issue
limma edgeR DESeq2
3.8 years ago aonghus • 0
3
votes
2
replies
2.1k
views
Filtering low coverage RRBS counts results in few reads. Any alternatives?
limma edgeR
updated 3.9 years ago by ▴ 10 • written 3.9 years ago by • 0
3
votes
2
replies
2.3k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 12 months ago by 53k • written 3.9 years ago by • 0
3
votes
4
replies
1.8k
views
edgeR shows different results for same dataset
edgeR
updated 3.9 years ago by 53k • written 4.0 years ago by • 0
1
vote
1
reply
2.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
2
votes
4
replies
2.0k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2 limma modelmatrix edgeR designmatrix
updated 4.0 years ago by 53k • written 4.1 years ago by • 0
2,031 results • Page 6 of 41
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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