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NanoString
•
reset
0
votes
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
3.0k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 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 3.3 years ago by
Michael Love
43k • written 3.3 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 18 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
5.4 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 5.6 years ago by
Gordon Smyth
52k • written 5.6 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
1.9k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
6.8 years ago • updated 6.1 years ago
SB
• 0
0
votes
5
replies
1.6k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 6.4 years ago by
James W. MacDonald
68k • written 6.4 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 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
casey.rimland
▴ 170
9
votes
13
replies
6.7k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
casey.rimland
▴ 170
1
vote
1
reply
1.3k
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 7.1 years ago by
Michael Love
43k • written 7.1 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
7.8 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
9.6 years ago
alakatos
▴ 130
24
votes
12
replies
13k
views
Nanostring analysis with limma
nanostring
limma
updated 10.0 years ago by
ker61
▴ 20 • written 10.0 years ago by
mali salmon
▴ 370
18 results • Page
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Comment: GSEA preranked analysis downstream of DEseq2
by
Ajay
• 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file
by
janwilseo
• 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
by
donnycrimson
• 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender
by
donnycrimson
• 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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