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LFC
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7
replies
2.2k
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LRT test followed by filtering based on LFC
deseq2
LFC
LRT
written 6.8 years ago by
sally.badawi
• 0
1
vote
1
reply
1.3k
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
stew
• 0
0
votes
1
reply
1.7k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
4.5 years ago
ayy2110
• 0
0
votes
6
replies
2.4k
views
large range of LFC in DESeq2
deseq2
lfc
betaprior
updated 3.1 years ago by
Michael Love
43k • written 7.0 years ago by
Mariaxi
• 0
17
votes
7
replies
16k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 8.4 years ago by
Michael Love
43k • written 8.4 years ago by
Anke Busch
▴ 10
6
votes
4
replies
3.5k
views
Identification of DEGs through limma analysis
limma
microarray
DEGs
p values
lfc
8.5 years ago
rkp
• 0
4
votes
14
replies
22k
views
standard error value (lfcSE) returned by DeSeq2
deseq2
deseq
lfc
lfcse
standard error
updated 8.7 years ago by
rraadd_8
• 0 • written 8.8 years ago by
tootiki
• 0
2
votes
1
reply
3.0k
views
Using Limma to identify any differences between multiple treatment groups (without making pairwise comparisons)
microarray
limma
multiple treatments
lfc
updated 9.6 years ago by
Aaron Lun
★ 29k • written 9.6 years ago by
brionyk9
• 0
8 results • Page
1 of 1
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Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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