Showing : degs • reset
0
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3
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616
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code syntax for DESeq2 to derive DEGs from a complicated contrast or interaction contrast?
DESeq2 Complicated.contrast DEGs
updated 19 months ago by 41k • written 19 months ago by • -60
-6
votes
4
replies
830
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
2
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3
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895
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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
2
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766
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Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
2.2 years ago Raito92 ▴ 60
0
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3
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949
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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 50k • written 2.7 years ago by ▴ 380
0
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20
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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
2
votes
1
reply
4.8k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.2 years ago by • 0 • written 5.3 years ago by ▴ 30
0
votes
2
replies
966
views
Deseq2 cooks filter for 2 replicates x 3 replicates
DESeq2 Nullcook'svalues 2x3 DEGs
3.1 years ago andreia ▴ 10
4
votes
5
replies
1.3k
views
DEseq2 results
heatmaps DEGs PCA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
2
votes
2
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1.0k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
3.3 years ago 2021yearsold • 0
0
votes
1
reply
819
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
3.8 years ago andreia ▴ 10
0
votes
2
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775
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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
1
reply
876
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
3.9 years ago tpm • 0
3
votes
2
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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
2
votes
4
replies
977
views
How to make grouping and contrast for multfactor design?
edger DEGs
4.3 years ago anikng ▴ 10
2
votes
3
replies
970
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
0
votes
2
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4.0k
views
Heatmap of selected genes
heatmap DEGs RNAseq DESeq2
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by • 0
4
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3
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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
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 50k • written 6.2 years ago by ▴ 30
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
6
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4
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2.7k
views
Identification of DEGs through limma analysis
limma microarray DEGs p values lfc
6.8 years ago rkp • 0
22 results • Page 1 of 1
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Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
I don't really have any additional suggestion here.
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Dear Michael, I tried all three ways (the orIginal, increasing the number of required samples,and subsetting (the countdata and metadata be…
Comment: DESeq2 - dispersion estimation when there is none by Michael Love 41k
The red line does assume that shape but the fact the black points show that pattern is discussed in the 2014 paper. > Some caution is warr…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
I don't really follow what you are saying. All you have to do is delete the NCBI.sqlite db and *re-run the script exactly as you did above.…
Comment: Methylation Analysis experiment design using Limma by hortense96 • 0
Thank you very much for your reply and your suggestion, as I'm having a bit of trouble finding information on how to manage this part of th…
Votes
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
Answer: OrgDb for maize
Answer: DESeq2 - dispersion estimation when there is none
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