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Nanostring
•
reset
0
votes
0
replies
711
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 2.3 years ago by
Michael Love
41k • written 2.3 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
0
votes
9
replies
1.5k
views
DESeq2 with nanostring data
deseq2
nanostring
4.4 years ago
acs1990
▴ 10
0
votes
4
replies
972
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
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
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
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
0
votes
5
replies
1.2k
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
1
reply
1.4k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.1 years ago
SB
• 0
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
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
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
8.6 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
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Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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