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NanoString
•
reset
0
votes
0
replies
1.5k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
3.0 years ago
Zhijie
• 0
0
votes
3
replies
3.4k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 3.5 years ago by
James W. MacDonald
68k • written 3.5 years ago by
junli1988
• 0
2
votes
3
replies
2.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter
DifferentialExpression
Housekeeping
DESeq2
NanoString
updated 4.0 years ago by
Michael Love
43k • written 4.0 years ago by
argonvibio
• 0
1
vote
5
replies
2.7k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
updated 17 months ago by
BioinfGuru
▴ 70 • written 4.6 years ago by
xiaofeiwang18266
▴ 60
0
votes
9
replies
2.3k
views
DESeq2 with nanostring data
deseq2
nanostring
6.1 years ago
acs1990
▴ 10
0
votes
4
replies
1.7k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 6.3 years ago by
Gordon Smyth
53k • written 6.3 years ago by
uridavid.akavia
• 0
0
votes
1
reply
2.3k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 5.7 years ago by
hermidalc
▴ 20 • written 6.4 years ago by
raf4
▴ 30
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
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 4 months ago by
James W. MacDonald
68k • written 6.5 years ago by
lim6432
▴ 60
0
votes
5
replies
2.0k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
Guillaume Robert
• 0
1
vote
1
reply
2.1k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
7.5 years ago • updated 6.8 years ago
SB
• 0
9
votes
15
replies
7.5k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 4 months ago by
Michael Love
43k • written 7.6 years ago by
casey.rimland
▴ 170
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
1
vote
1
reply
1.4k
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 7.8 years ago by
Michael Love
43k • written 7.8 years ago by
kim.malek88
• 0
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
3
votes
8
replies
4.3k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2
variancestabilizingtransformation
nanostring
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
johnmcma
▴ 10
2
votes
0
replies
2.4k
views
NanoString Data Normalization Revisited
nanostring
normalization
10.3 years ago
alakatos
▴ 130
24
votes
12
replies
14k
views
Nanostring analysis with limma
nanostring
limma
updated 10.7 years ago by
ker61
▴ 20 • written 10.7 years ago by
mali salmon
▴ 370
18 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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