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NanoString
•
reset
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
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
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
0
votes
9
replies
1.6k
views
DESeq2 with nanostring data
deseq2
nanostring
4.4 years ago
acs1990
▴ 10
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
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
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
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
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
4
replies
974
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
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
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
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
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
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
0
votes
0
replies
716
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
15 months ago
Zhijie
• 0
2
votes
0
replies
1.9k
views
NanoString Data Normalization Revisited
nanostring
normalization
8.6 years ago
alakatos
▴ 130
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
18 results • Page
1 of 1
Recent ...
Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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