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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
968
views
How to make grouping and contrast for multfactor design?
edger
DEGs
4.3 years ago
anikng
▴ 10
2
votes
3
replies
964
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
943
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
888
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
872
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler
Bioconductor
R
DEGs
3.9 years ago
tpm
• 0
-6
votes
4
replies
828
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
813
views
mircomb analysis from deg's list
mircomb
mrna
mirna
degs
interaction
3.8 years ago
andreia
▴ 10
0
votes
2
replies
772
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
760
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
612
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: significant difference of p-values with dream() after updating VariancePartition
by
gabriel.hoffman
▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded
by
W. Evan Johnson
▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis
by
Alejandro Reyes
★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object
by
Alejandro Reyes
★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Answer: rlog transformation
by
Michael Love
41k
It is dependent on the other samples in the dataset.
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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