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Showing :
expression
•
reset
5
votes
8
replies
2.0k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression
R
filtering
limma
21 months ago • updated 18 months ago
mohammedtoufiq91
▴ 10
0
votes
0
replies
474
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
22 months ago
Jonathan
• 0
0
votes
1
reply
1.2k
views
Re-normalize microarray dataset in R
microarray
quantile
expression
R
Normalization
updated 2.9 years ago by
Konstantinos Yeles
▴ 80 • written 2.9 years ago by
mohammedtoufiq91
▴ 10
1
vote
1
reply
1.1k
views
Table expression data from GEO file
GEO
expression
GEOquery
updated 4.1 years ago by
Robert Castelo
★ 3.3k • written 4.1 years ago by
lsbew
• 0
1
vote
9
replies
2.0k
views
Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs
RNA-Seq
Isoforms
DTU
expression
updated 4.9 years ago by
fruce_ki
▴ 20 • written 4.9 years ago by
UserAnonyme
• 0
1
vote
2
replies
749
views
Two factors design with DESEq2
deseq2
genes
expression
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
UserAnonyme
• 0
7
votes
3
replies
3.4k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
kushshah
▴ 10
0
votes
6
replies
1.4k
views
variancePartition - testing for individuals
variance
formula
expression
updated 5.4 years ago by
mikhael.manurung
▴ 280 • written 5.4 years ago by
rina
▴ 30
0
votes
0
replies
1.6k
views
Job:
Research Associate, Cambridge, UK - Oesophageal Cancer ICGC project
job
sequencing
methylation
expression
Job
9.3 years ago
Andy Lynch
▴ 120
6
votes
5
replies
1.9k
views
Limma ebayes returns a list with Affy pd.hugene.2.0.st arrays
ebayes
expression
affymetrix
pd.hugene.2.0.st
limma
updated 9.4 years ago by
Gordon Smyth
51k • written 9.4 years ago by
Paulo Nuin
▴ 200
10 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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swbarnes2
★ 1.4k
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to
Stephanie M. Gogarten
▴ 870
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Jonathan
▴ 10
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Frederico Moraes Ferreira
▴ 100
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richardallenfriedmanbrooklyn
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