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degs
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0
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20
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2.4k
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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
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps
DEGs
PCA
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
MOHAMMAD
• 0
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
Gordon Smyth
50k • written 6.3 years ago by
lawarde.ankita1
▴ 30
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
2
votes
4
replies
992
views
How to make grouping and contrast for multfactor design?
edger
DEGs
4.3 years ago
anikng
▴ 10
-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
2
votes
3
replies
907
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR
DEGs
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
RR
• 0
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
Michael Love
41k • written 4.5 years ago by
gmchaput
• 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
Gordon Smyth
50k • written 5.8 years ago by
takumima
▴ 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
Gordon Smyth
50k • written 2.7 years ago by
Ming
▴ 380
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
Michael Love
41k • written 20 months ago by
Mike
• -60
0
votes
2
replies
4.1k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 4.8 years ago by
mikhael.manurung
▴ 270 • written 4.8 years ago by
danikadigiacomo
• 0
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
Gordon Smyth
50k • written 4.3 years ago by
anikng
▴ 10
0
votes
2
replies
790
views
mirna-mrna interation mircomb (from DEGs and DEMs lists)
deseq2
mircomb
degs
dems
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
andreia
▴ 10
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
0
votes
2
replies
983
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2
Nullcook'svalues
2x3
DEGs
3.1 years ago
andreia
▴ 10
0
votes
2
replies
779
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR
DEGs
DESEQ2
RNASeqData
2.2 years ago
Raito92
▴ 60
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 2.3 years ago by
rickap
• 0 • written 5.3 years ago by
aishu.jp
▴ 30
0
votes
1
reply
883
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler
Bioconductor
R
DEGs
3.9 years ago
tpm
• 0
2
votes
1
reply
4.9k
views
EnhancedVolcano Label Question
RNASeq
EnhancedVolcano
DEGs
updated 2.9 years ago by
Kevin Blighe
★ 3.9k • written 2.9 years ago by
robledoj13
• 0
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
Aaron Lun
★ 28k • written 6.7 years ago by
baus87
• 0
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
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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