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Nanostring
•
reset
0
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0
replies
738
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
16 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
1.6k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter
DifferentialExpression
Housekeeping
DESeq2
NanoString
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
argonvibio
• 0
1
vote
4
replies
1.6k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.9 years ago
xiaofeiwang18266
▴ 50
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 6 months ago by
georgersmith
• 0 • written 4.8 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 4.8 years ago by
raf4
▴ 20
0
votes
9
replies
1.6k
views
DESeq2 with nanostring data
deseq2
nanostring
4.4 years ago
acs1990
▴ 10
0
votes
4
replies
988
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
8.6k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.3 years ago by
Clara
• 0 • written 4.8 years ago by
lim6432
▴ 50
1
vote
1
reply
1.5k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.1 years ago
SB
• 0
0
votes
5
replies
1.3k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 5.4 years ago by
James W. MacDonald
65k • written 5.4 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
5.5k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 5.9 years ago by
Michael Love
42k • 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
42k • 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 7.1 years ago by
Michael Love
42k • written 7.1 years ago by
johnmcma
▴ 10
2
votes
0
replies
1.9k
views
NanoString Data Normalization Revisited
nanostring
normalization
8.6 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
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Replies
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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