Showing : experimental design • reset
6
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6
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4.2k
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Limma multi-group analysis - General F-test
limma experimental design
updated 4.0 years ago by 51k • written 4.0 years ago by ▴ 10
0
votes
1
reply
694
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
1
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2
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820
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Call DE genes on Unbalanced design with controls
edger experimental design
5.1 years ago timedreamer ▴ 10
0
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4
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981
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DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
5.6 years ago Maithê Barros ▴ 10
1
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9
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1.6k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ★ 1.5k
0
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0
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914
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Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
5.7 years ago dezer ▴ 10
2
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6
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1.1k
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DESeq2 Gene Expression Set up: Behavior vs Age
deseq2 experimental design
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
4
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2
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1.1k
views
How does the function model.matrix (to define experimental design) really works ?
experimental design model.matrix edger
updated 6.2 years ago by ★ 7.9k • written 6.2 years ago by ▴ 20
1
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2
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1.4k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
0
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1
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3.0k
views
DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
6
votes
1
reply
11k
views
DESeq2 interaction term in two-factor design, which contrasts?
deseq2 experimental design interaction model
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 30
1
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2
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4.5k
views
Multiple comparisons for DE analysis with DESeq2
deseq2 mirna-seq experimental design differential expression
updated 7.1 years ago by ▴ 680 • written 7.1 years ago by ▴ 10
1
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2
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1.5k
views
Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
EdgeR RNAseq experimental design glm
updated 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
0
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1
reply
948
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Genotypic difference design using deseq2
Deseq2 genotype experimental design
updated 7.3 years ago by 42k • written 7.3 years ago by ▴ 90
5
votes
2
replies
1.8k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 7.6 years ago by 42k • written 7.6 years ago by ▴ 20
2
votes
2
replies
1.3k
views
EdgeR experimental design matrix
edger differential gene expression experimental design
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.5 years ago by 42k • written 8.5 years ago by ▴ 60
5
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7
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2.1k
views
what conditions affect my gene (with limma?)
limma geo experimental design
updated 8.8 years ago by 51k • written 8.8 years ago by • 0
4
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3
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3.0k
views
DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 9.1 years ago by 42k • written 9.1 years ago by ▴ 40
1
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2
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1.7k
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qRT-PCR Sample Maximization software analysis and proper experimental design advice
qPCR Sample Maximization Analysis Experimental Design qRT-PCR
updated 9.1 years ago by 51k • written 9.1 years ago by ▴ 450
0
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4
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2.0k
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Question: DESeq2 nested design, multifactor test
deseq2 experimental design
9.1 years ago Shucong Li ▴ 60
21 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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