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lncRNA
•
reset
2
votes
4
replies
3.4k
views
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
diffGeneAnalysis
lncRNA
6 months ago
John
▴ 10
0
votes
0
replies
666
views
how to convert lncRNA probe name or mRNA probe name to gene symbol
lncRNA
probeID
mRNA
genesymbol
2.9 years ago
Sooni
▴ 10
3
votes
3
replies
2.1k
views
Recount data for unannotated genes
recount
RNAseq
gencode
lncRNA
gene annotation
updated 6.8 years ago by
chris.wilks
▴ 70 • written 6.8 years ago by
francesco.gandolfi
▴ 20
0
votes
1
reply
2.1k
views
TPM and FPKM for lncRNA
GenomicFeatures
TPM
FPKM
lncRNA
7.6 years ago
Ina Hoeschele
▴ 620
0
votes
2
replies
4.2k
views
lncRNA annotation for featureCouns and STAR
lncRNA
featureCounts
STAR
annotation
updated 7.6 years ago by
Wei Shi
★ 3.6k • written 7.6 years ago by
inah
▴ 10
0
votes
2
replies
2.0k
views
R packages for differential expression analysis of raw data from arraystar microarrays
microarray
lncrna
microrna
mrna
raw data
updated 8.1 years ago by
Axel Klenk
★ 1.1k • written 8.1 years ago by
ntagaras
• 0
0
votes
3
replies
3.9k
views
Annotation DB for ArrayStar lncRNA arrays
arraystar
lncRNA
annotation
annotationdbi
updated 10.4 years ago by
xiangy7
• 0 • written 10.8 years ago by
Kevin Coombes
▴ 430
7 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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Thomas Girke
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