Showing : degs • reset
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.3 years ago by • 0 • written 5.3 years ago by ▴ 30
2
votes
1
reply
4.9k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
0
votes
2
replies
4.1k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 4.8 years ago by ▴ 270 • written 4.8 years ago by • 0
6
votes
4
replies
2.7k
views
Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
6.9 years ago rkp • 0
0
votes
20
replies
2.4k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2 DEGs
2.8 years ago Ming ▴ 380
3
votes
2
replies
2.3k
views
How to deal with elimination of genes when using filterByExpr function?
edger DEGs normalization
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 10
3
votes
5
replies
2.1k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma heatmap DEGs
updated 6.3 years ago by 50k • written 6.3 years ago by ▴ 30
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
4
votes
3
replies
1.1k
views
Differential profile for only one normal - tumor pair
edger degs paired design
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 10
3
votes
1
reply
1.1k
views
Common dispersion value using edgeR for DEGs analysis
edgeR DEGS common disperion
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
2
votes
2
replies
1.0k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
3.3 years ago 2021yearsold • 0
2
votes
4
replies
992
views
How to make grouping and contrast for multfactor design?
edger DEGs
4.3 years ago anikng ▴ 10
2
votes
3
replies
991
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 4.5 years ago by 41k • written 4.5 years ago by • 0
0
votes
2
replies
984
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
3.1 years ago andreia ▴ 10
0
votes
3
replies
960
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 2.2 years ago by 50k • written 2.7 years ago by ▴ 380
2
votes
3
replies
908
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
0
votes
1
reply
883
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
3.9 years ago tpm • 0
-6
votes
4
replies
839
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
20 months ago Mike • -60
0
votes
1
reply
835
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
3.9 years ago • updated 3.8 years ago andreia ▴ 10
0
votes
2
replies
791
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2 mircomb degs dems
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 10
0
votes
2
replies
780
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
2.2 years ago Raito92 ▴ 60
0
votes
3
replies
627
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 20 months ago by 41k • written 20 months ago by • -60
22 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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