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DEGS
•
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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
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
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
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
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
2
votes
3
replies
975
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
2
votes
4
replies
979
views
How to make grouping and contrast for multfactor design?
edger
DEGs
4.3 years ago
anikng
▴ 10
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
1
reply
822
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
3.8 years ago
andreia
▴ 10
0
votes
2
replies
776
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
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps
DEGs
PCA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
MOHAMMAD
• 0
0
votes
2
replies
969
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
617
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
0
votes
3
replies
951
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
0
votes
2
replies
767
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR
DEGs
DESEQ2
RNASeqData
2.2 years ago
Raito92
▴ 60
2
votes
1
reply
4.8k
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
2
votes
3
replies
897
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
-6
votes
4
replies
832
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
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
877
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler
Bioconductor
R
DEGs
3.9 years ago
tpm
• 0
22 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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Gordon Smyth
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