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NanoString
•
reset
0
votes
0
replies
341
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
8 months ago
Zhijie
• 0
0
votes
3
replies
1.3k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 14 months ago by
James W. MacDonald
63k • written 14 months ago by
junli1988
• 0
2
votes
3
replies
1.1k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter
DifferentialExpression
Housekeeping
DESeq2
NanoString
updated 20 months ago by
Michael Love
40k • written 20 months ago by
argonvibio
• 0
1
vote
4
replies
1.1k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.3 years ago
xiaofeiwang18266
▴ 50
2
votes
4
replies
1.4k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 2.3 years ago by
anastazie.d
▴ 20 • written 4.2 years ago by
lim6432
▴ 50
0
votes
1
reply
1.3k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 3.4 years ago by
hermidalc
▴ 20 • written 4.1 years ago by
raf4
▴ 20
0
votes
9
replies
1.3k
views
DESeq2 with nanostring data
deseq2
nanostring
3.8 years ago
acs1990
▴ 10
0
votes
4
replies
774
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 4.0 years ago by
Gordon Smyth
48k • written 4.0 years ago by
uridavid.akavia
• 0
16
votes
40
replies
6.7k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 21 months ago by
Clara
• 0 • written 4.2 years ago by
lim6432
▴ 50
1
vote
1
reply
1.2k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.2 years ago • updated 4.5 years ago
SB
• 0
0
votes
5
replies
1.0k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 4.8 years ago by
James W. MacDonald
63k • written 4.8 years ago by
Guillaume Robert
• 0
1
vote
6
replies
1.6k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 5.3 years ago by
James W. MacDonald
63k • written 5.3 years ago by
casey.rimland
▴ 150
8
votes
13
replies
4.7k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 5.3 years ago by
Michael Love
40k • written 5.3 years ago by
casey.rimland
▴ 150
1
vote
1
reply
952
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 5.5 years ago by
Michael Love
40k • written 5.5 years ago by
kim.malek88
• 0
0
votes
0
replies
1.1k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
6.2 years ago
c.kohler
• 0
3
votes
8
replies
3.1k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2
variancestabilizingtransformation
nanostring
updated 6.5 years ago by
Michael Love
40k • written 6.5 years ago by
johnmcma
▴ 10
2
votes
0
replies
1.7k
views
NanoString Data Normalization Revisited
nanostring
normalization
8.0 years ago
alakatos
▴ 130
24
votes
12
replies
11k
views
Nanostring analysis with limma
nanostring
limma
updated 8.4 years ago by
ker61
▴ 20 • written 8.4 years ago by
mali salmon
▴ 370
18 results • Page
1 of 1
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Replies
Comment: using featureCounts (Subread) to count only spliced reads per gene - behavior of
by
Gregory
• 0
Thanks for the prompt response, Gordon. I'm looking for count at the gene level - the gene id is the meta feature, so one row per gene in …
Comment: DiffBind handling of replicates and consensus
by
Rory Stark
★ 5.0k
You may want to try different values for the `normalize` parameter: dbObj <- dba.normalize(DBA = dbObj, library = "RiP", normalize=DBA…
Comment: DiffBind: dba.plotProfile(profiles)
by
Rory Stark
★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles)
by
Dorien
▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor
by
shepherl
3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Votes
Comment: DiffBind: dba.plotProfile(profiles)
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
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