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michael love
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3
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993
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DESeq2 time course with two genotypes
deseq2
timecourse
michael love
multiple time points
4.7 years ago
cp1015
• 0
0
votes
4
replies
753
views
DESeq2 Design Formula
DESeq2
michael love
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
gkuffel
▴ 10
0
votes
1
reply
1.1k
views
DESeq2 PCA plotting
deseq2
michael love
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
sam.far.7
• 0
1
vote
11
replies
1.6k
views
Need help with DESeq2's contrast feature
deseq2
michael love
updated 5.8 years ago by
Michael Love
42k • written 5.8 years ago by
Ashu
▴ 10
2
votes
3
replies
1.5k
views
DESeq2 for time series using time as continuous and looking at effect of time on DE
deseq2
timecourse
multiple time points
mlr
michael love
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
ap874
• 0
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love
Salmon
tximport
tx2gene
updated 6.3 years ago by
Michael Love
42k • written 6.3 years ago by
pvd2107
▴ 30
6 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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