Showing : degs • reset
0
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3
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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
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4
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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
2
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3
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896
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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
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2
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767
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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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951
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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
967
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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 3.2 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
820
views
mircomb analysis from deg's list
mircomb mrna mirna degs interaction
3.8 years ago andreia ▴ 10
0
votes
2
replies
776
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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
877
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
978
views
How to make grouping and contrast for multfactor design?
edger DEGs
4.3 years ago anikng ▴ 10
2
votes
3
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973
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
votes
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
votes
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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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
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?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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