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Nanostring
•
reset
0
votes
0
replies
697
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
15 months ago
Zhijie
• 0
0
votes
3
replies
2.1k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
junli1988
• 0
2
votes
3
replies
1.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter
DifferentialExpression
Housekeeping
DESeq2
NanoString
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
argonvibio
• 0
1
vote
4
replies
1.5k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.8 years ago
xiaofeiwang18266
▴ 50
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 5 months ago by
georgersmith
• 0 • written 4.7 years ago by
lim6432
▴ 50
0
votes
1
reply
1.6k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 4.0 years ago by
hermidalc
▴ 20 • written 4.7 years ago by
raf4
▴ 20
0
votes
9
replies
1.5k
views
DESeq2 with nanostring data
deseq2
nanostring
4.3 years ago
acs1990
▴ 10
0
votes
4
replies
962
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
uridavid.akavia
• 0
16
votes
40
replies
8.5k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.3 years ago by
Clara
• 0 • written 4.7 years ago by
lim6432
▴ 50
1
vote
1
reply
1.4k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.0 years ago
SB
• 0
0
votes
5
replies
1.2k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 5.3 years ago by
James W. MacDonald
65k • written 5.3 years ago by
Guillaume Robert
• 0
1
vote
6
replies
1.9k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
casey.rimland
▴ 150
8
votes
13
replies
5.4k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
casey.rimland
▴ 150
1
vote
1
reply
1.1k
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 6.1 years ago by
Michael Love
41k • written 6.1 years ago by
kim.malek88
• 0
0
votes
0
replies
1.3k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
6.8 years ago
c.kohler
• 0
3
votes
8
replies
3.4k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2
variancestabilizingtransformation
nanostring
updated 7.0 years ago by
Michael Love
41k • written 7.0 years ago by
johnmcma
▴ 10
2
votes
0
replies
1.9k
views
NanoString Data Normalization Revisited
nanostring
normalization
8.5 years ago
alakatos
▴ 130
24
votes
12
replies
12k
views
Nanostring analysis with limma
nanostring
limma
updated 9.0 years ago by
ker61
▴ 20 • written 9.0 years ago by
mali salmon
▴ 370
18 results • Page
1 of 1
Recent ...
Replies
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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