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NanoString
•
reset
0
votes
0
replies
1.1k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
2.1 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 6 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 15 months ago by
georgersmith
• 0 • written 5.5 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 4.8 years ago by
hermidalc
▴ 20 • written 5.5 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
1.2k
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 3.1 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
1.5k
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
6.5k
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 9.8 years ago by
mali salmon
▴ 370
18 results • Page
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Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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