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Nanostring
•
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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
2.3 years ago
Zhijie
• 0
0
votes
3
replies
2.9k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
junli1988
• 0
2
votes
3
replies
2.2k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter
DifferentialExpression
Housekeeping
DESeq2
NanoString
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
argonvibio
• 0
1
vote
5
replies
2.3k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
updated 8 months ago by
BioinfGuru
▴ 70 • written 3.8 years ago by
xiaofeiwang18266
▴ 60
3
votes
6
replies
2.4k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 17 months ago by
georgersmith
• 0 • written 5.7 years ago by
lim6432
▴ 50
0
votes
1
reply
2.1k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 5.0 years ago by
hermidalc
▴ 20 • written 5.7 years ago by
raf4
▴ 30
0
votes
9
replies
2.0k
views
DESeq2 with nanostring data
deseq2
nanostring
5.3 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 5.5 years ago by
Gordon Smyth
52k • written 5.5 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 3.3 years ago by
Clara
▴ 10 • written 5.7 years ago by
lim6432
▴ 50
1
vote
1
reply
1.8k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
6.7 years ago • updated 6.0 years ago
SB
• 0
0
votes
5
replies
1.6k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 6.3 years ago by
James W. MacDonald
68k • written 6.3 years ago by
Guillaume Robert
• 0
1
vote
6
replies
2.5k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
casey.rimland
▴ 170
9
votes
13
replies
6.7k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
casey.rimland
▴ 170
1
vote
1
reply
1.3k
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 7.0 years ago by
Michael Love
43k • written 7.0 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
7.7 years ago
c.kohler
• 0
3
votes
8
replies
4.0k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2
variancestabilizingtransformation
nanostring
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
johnmcma
▴ 10
2
votes
0
replies
2.2k
views
NanoString Data Normalization Revisited
nanostring
normalization
9.5 years ago
alakatos
▴ 130
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring
limma
updated 9.9 years ago by
ker61
▴ 20 • written 10.0 years ago by
mali salmon
▴ 370
18 results • Page
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Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly?
by
James W. MacDonald
68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset
by
ATpoint
★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
ATpoint
★ 4.8k
That plot looks extremely worrying. You have very unbalanced DE profiles and clearly two populations of peaks on the right. I would make su…
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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