Showing : dge • reset
7
votes
6
replies
412
views
Batch Effect Correction, Gene Filtering
DGE limma
updated 28 days ago by 50k • written 28 days ago by • 0
0
votes
3
replies
469
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE DESeq2
6 months ago ruba-mahmoud • 0
1
vote
3
replies
615
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
1
reply
443
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
1
reply
789
views
DGE genes are not available in GSEA
dge gsea
updated 16 months ago by ★ 3.9k • written 16 months ago by • 0
5
votes
6
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1.5k
views
How to calculate dispersion DESeq2 - Step by Step
DGE DESeq2 Differential
2.7 years ago • updated 2.6 years ago Zeke Smith ▴ 10
1
vote
1
reply
709
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome organoids DGE DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
1
vote
2
replies
861
views
How to construct matrix and fit linear model for this microarray?
microarray dge matrix makecontrasts limma
updated 3.8 years ago by 50k • written 3.8 years ago by ▴ 10
5
votes
10
replies
1.3k
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 3.8 years ago by 41k • written 3.8 years ago by • 0
3
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8
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1.2k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
votes
2
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850
views
Longitudinal Time-Course microarray experiment with two time points
edge DGE microarray
updated 4.4 years ago by 50k • written 4.4 years ago by • 0
1
vote
5
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1.2k
views
edgeR or DESeq2 between duplicated chromosomes in the same individual
deseq2 edgeR normalization DGE
updated 4.5 years ago by 50k • written 4.5 years ago by ▴ 10
0
votes
4
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2.6k
views
edgeR DGEList and design matrix
edger DGE
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by • 0
3
votes
7
replies
2.2k
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq DGE edger
updated 4.8 years ago by 50k • written 4.9 years ago by • 0
0
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0
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891
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
5.4 years ago lkianmehr • 0
3
votes
4
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1.9k
views
DGE matrix annotation
DGE DESeq2 AnnotationDbi
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
3
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1.7k
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger DGE coef
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
4
votes
8
replies
1.8k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq edger DGE no replicates
6.7 years ago Stefany Solano • 0
5
votes
4
replies
1.3k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 6.9 years ago by • 0 • written 6.9 years ago by ▴ 40
12
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10
replies
6.4k
views
edgeR glmLRT with test="F"?
edger dge differential expression
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ★ 7.9k
21 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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