Showing : DEGS • reset
0
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3
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612
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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
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
2
votes
3
replies
888
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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
replies
760
views
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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943
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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
votes
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
4.7k
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
962
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
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
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 41k • written 3.8 years ago by ▴ 10
0
votes
1
reply
872
views
compareCluster error: On clusterProfiler DEGs enrichments analysis
clusterProfiler Bioconductor R DEGs
3.9 years ago tpm • 0
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 50k • written 4.2 years ago by ▴ 10
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 41k • written 4.4 years ago by • 0
0
votes
2
replies
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
votes
3
replies
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
votes
4
replies
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: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist by Sherin • 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Votes
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
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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