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nanostringdiff
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2.2k
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
2.6 years ago
pg45863
▴ 10
0
votes
2
replies
1.9k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
2.7 years ago
pg45863
▴ 10
0
votes
1
reply
1.2k
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 3.0 years ago by
James W. MacDonald
68k • written 3.0 years ago by
Aleksandra
• 0
0
votes
2
replies
908
views
NanoStringDiff contrast vectors
NanoStringDiff
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Paraskevi
• 0
0
votes
0
replies
1.0k
views
NanoStringDiff
DifferentialExpression
NanoStringDiff
4.1 years ago
sanrie10
• 0
5
votes
7
replies
2.5k
views
Nanostringdiff - defining contrast values for blocking variables in glm
limma
edgeR
DESeq2
NanoStringDiff
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
reberya
• 0
3
votes
2
replies
1.5k
views
R NanoStringDiff: DE analysis, from 2 group comparison method how "logFC" generated?
Nan
NanoStringDiff
4.5 years ago
choijamts
• 0
3
votes
6
replies
2.7k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 2.2 years ago by
georgersmith
• 0 • written 6.5 years ago by
lim6432
▴ 60
0
votes
0
replies
1.1k
views
NanoStringDiff - housekeeping genes variation
NanoStringDiff
4.8 years ago
YM
• 0
1
vote
1
reply
1.4k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 5.2 years ago by
Laurent Gatto
1.6k • written 5.2 years ago by
Pedro
▴ 10
1
vote
7
replies
1.8k
views
NanoStringDiff glm.LRT not finishing after 20 hours
NanoStringDiff
6.0 years ago
stephen.pollo
• 0
0
votes
2
replies
1.3k
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 years ago by
Guillaume Robert
• 0
3
votes
3
replies
2.0k
views
NanoStringDiff counts not numeric
NanoStringDiff
updated 24 months ago by
pjanas
• 0 • written 6.7 years ago by
noelleenright
▴ 10
1
vote
6
replies
2.9k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 7.6 years ago by
James W. MacDonald
68k • written 7.6 years ago by
casey.rimland
▴ 170
0
votes
0
replies
1.8k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
8.5 years ago
c.kohler
• 0
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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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