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DEGs
•
reset
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 2.2 years ago by
rickap
• 0 • written 5.3 years ago by
aishu.jp
▴ 30
2
votes
1
reply
4.7k
views
EnhancedVolcano Label Question
RNASeq
EnhancedVolcano
DEGs
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
robledoj13
• 0
0
votes
2
replies
4.0k
views
Heatmap of selected genes
heatmap
DEGs
RNAseq
DESeq2
updated 4.7 years ago by
mikhael.manurung
▴ 270 • written 4.7 years ago by
danikadigiacomo
• 0
6
votes
4
replies
2.7k
views
Identification of DEGs through limma analysis
limma
microarray
DEGs
p values
lfc
6.8 years ago
rkp
• 0
0
votes
20
replies
2.3k
views
DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2
DEGs
2.8 years ago • updated 2.7 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 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
anikng
▴ 10
3
votes
5
replies
2.1k
views
DEGs of microarray Data and hierarchical clustering and visualizing using heatmap
limma
heatmap
DEGs
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
lawarde.ankita1
▴ 30
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps
DEGs
PCA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 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
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
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
970
views
How to make grouping and contrast for multfactor design?
edger
DEGs
4.3 years ago
anikng
▴ 10
2
votes
3
replies
966
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2
rrpp
DEGs
RNAseq
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
gmchaput
• 0
0
votes
2
replies
962
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
946
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq
edgeR
DEGs
updated 2.1 years ago by
Gordon Smyth
50k • written 2.7 years ago by
Ming
▴ 380
2
votes
3
replies
889
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
0
votes
1
reply
873
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler
Bioconductor
R
DEGs
3.9 years ago
tpm
• 0
-6
votes
4
replies
829
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast
edgeR
DEGs
19 months ago
Mike
• -60
0
votes
1
reply
815
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
3.8 years ago
andreia
▴ 10
0
votes
2
replies
773
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
0
votes
2
replies
763
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
614
views
code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2
Complicated.contrast
DEGs
updated 19 months ago by
Michael Love
41k • written 19 months ago by
Mike
• -60
22 results • Page
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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