Showing : degs • reset
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.8 years ago by ▴ 30
0
votes
3
replies
799
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 2.2 years ago by 42k • written 2.2 years ago by • -60
-6
votes
4
replies
982
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
2.2 years ago Mike • -60
2
votes
3
replies
1.1k
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 2.6 years ago by 51k • written 2.6 years ago by • 0
0
votes
2
replies
982
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
2.8 years ago Raito92 ▴ 60
0
votes
3
replies
1.1k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 2.7 years ago by 51k • written 3.3 years ago by ▴ 380
0
votes
20
replies
2.9k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
3.4 years ago • updated 3.3 years ago Ming ▴ 380
2
votes
1
reply
6.9k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
0
votes
2
replies
1.2k
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
3.6 years ago andreia ▴ 10
4
votes
5
replies
1.6k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
2
votes
2
replies
1.2k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
3.9 years ago 2021yearsold • 0
0
votes
1
reply
977
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
4.4 years ago andreia ▴ 10
0
votes
2
replies
942
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2 mircomb degs dems
updated 4.4 years ago by 42k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
4.4 years ago tpm • 0
3
votes
2
replies
2.9k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 4.8 years ago by 51k • written 4.8 years ago by ▴ 10
2
votes
4
replies
1.2k
views
How to make grouping and contrast for multfactor design?
edger DEGs
4.9 years ago • updated 4.8 years ago anikng ▴ 10
2
votes
3
replies
1.2k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
votes
2
replies
4.5k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by • 0
4
votes
3
replies
1.3k
views
Differential profile for only one normal - tumor pair
edger degs paired design
updated 6.4 years ago by 51k • written 6.4 years ago by ▴ 10
3
votes
5
replies
2.3k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma heatmap DEGs
updated 6.8 years ago by 51k • written 6.8 years ago by ▴ 30
3
votes
1
reply
1.2k
views
Common dispersion value using edgeR for DEGs analysis
edgeR DEGS common disperion
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
6
votes
4
replies
3.0k
views
Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
7.4 years ago rkp • 0
22 results • Page 1 of 1
Recent ...
Replies
Comment: Appropriate ways to filter counts data for voom/limma by dorothylminter • 0
The proper way to filter count data for voom/limma emphasizes the importance of choosing the right filtering technique to enhance detection…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Comment: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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