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nanostring
•
reset
0
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0
replies
1.2k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
2.2 years ago
Zhijie
• 0
0
votes
3
replies
2.8k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
junli1988
• 0
2
votes
3
replies
2.1k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter
DifferentialExpression
Housekeeping
DESeq2
NanoString
updated 3.1 years ago by
Michael Love
43k • written 3.1 years ago by
argonvibio
• 0
1
vote
5
replies
2.2k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
updated 7 months ago by
BioinfGuru
▴ 70 • written 3.7 years ago by
xiaofeiwang18266
▴ 50
3
votes
6
replies
2.3k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 16 months ago by
georgersmith
• 0 • written 5.6 years ago by
lim6432
▴ 50
0
votes
1
reply
2.0k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 4.9 years ago by
hermidalc
▴ 20 • written 5.6 years ago by
raf4
▴ 30
0
votes
9
replies
1.9k
views
DESeq2 with nanostring data
deseq2
nanostring
5.2 years ago
acs1990
▴ 10
0
votes
4
replies
1.3k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 5.4 years ago by
Gordon Smyth
52k • written 5.4 years ago by
uridavid.akavia
• 0
16
votes
40
replies
11k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 3.2 years ago by
Clara
▴ 10 • written 5.6 years ago by
lim6432
▴ 50
1
vote
1
reply
1.8k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
6.6 years ago • updated 5.9 years ago
SB
• 0
0
votes
5
replies
1.6k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 6.2 years ago by
James W. MacDonald
68k • written 6.2 years ago by
Guillaume Robert
• 0
1
vote
6
replies
2.4k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
casey.rimland
▴ 170
9
votes
13
replies
6.6k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
casey.rimland
▴ 170
1
vote
1
reply
1.3k
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
kim.malek88
• 0
0
votes
0
replies
1.6k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
7.6 years ago
c.kohler
• 0
3
votes
8
replies
3.9k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2
variancestabilizingtransformation
nanostring
updated 7.9 years ago by
Michael Love
43k • written 7.9 years ago by
johnmcma
▴ 10
2
votes
0
replies
2.1k
views
NanoString Data Normalization Revisited
nanostring
normalization
9.4 years ago
alakatos
▴ 130
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring
limma
updated 9.8 years ago by
ker61
▴ 20 • written 9.9 years ago by
mali salmon
▴ 370
18 results • Page
1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output
by
ATpoint
★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression
by
Jane
• 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga
by
Jane
• 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output
by
Matthew McCormack
▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to
by
ATpoint
★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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