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gene expression
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0
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1.1k
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Help with generating network from gene expression data
gene expression
network
cytoscape
6.4 years ago
torgeirous
• 0
1
vote
9
replies
3.7k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma
gene expression
confounding
adjustment
paired
8.6 years ago
Loodramon
• 0
1
vote
1
reply
2.6k
views
sva and svaseq for unsupervised analysis of expression data
sva
combat
gene expression
batch effect
rnaseq
updated 8.8 years ago by
Jeff Leek
▴ 650 • written 8.8 years ago by
Farshad Farshidfar
▴ 10
0
votes
2
replies
3.0k
views
barplot with ggplot2 for gene expression
ggplot2
barplot
gene expression
gene expression
updated 8.8 years ago by
James W. MacDonald
66k • written 8.8 years ago by
alakatos
▴ 130
4 results • Page
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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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