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Nanostring
•
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0
votes
0
replies
757
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA
Normalization
BatchEffect
GSVAdata
NanoString
16 months ago
Zhijie
• 0
0
votes
3
replies
2.2k
views
[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet
Assay
NanoString
Error
Data
updated 22 months ago by
James W. MacDonald
66k • written 22 months ago by
junli1988
• 0
2
votes
3
replies
1.6k
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
42k • written 2.3 years ago by
argonvibio
• 0
1
vote
4
replies
1.6k
views
how to plot multiple RLEs on same plot?
plotRLE
Nanostring
RUVSeq
DESEQ2
2.9 years ago
xiaofeiwang18266
▴ 50
3
votes
6
replies
1.9k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 6 months ago by
georgersmith
• 0 • written 4.8 years ago by
lim6432
▴ 50
0
votes
1
reply
1.6k
views
Application of RUV to a small Nanostring dataset
RUV
Nanostring
RUV-III
updated 4.1 years ago by
hermidalc
▴ 20 • written 4.8 years ago by
raf4
▴ 20
0
votes
9
replies
1.6k
views
DESeq2 with nanostring data
deseq2
nanostring
4.4 years ago
acs1990
▴ 10
0
votes
4
replies
1.0k
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
16
votes
40
replies
8.7k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.4 years ago by
Clara
• 0 • written 4.8 years ago by
lim6432
▴ 50
1
vote
1
reply
1.5k
views
GSVA with NanoString nCounter data
GSVA
Nanostring
5.8 years ago • updated 5.1 years ago
SB
• 0
0
votes
5
replies
1.3k
views
NanoStringDiff analysis with confounding factors
differential gene expression
nanostring
confounding factors
updated 5.4 years ago by
James W. MacDonald
66k • written 5.4 years ago by
Guillaume Robert
• 0
1
vote
6
replies
2.0k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 6.0 years ago by
James W. MacDonald
66k • written 6.0 years ago by
casey.rimland
▴ 150
8
votes
13
replies
5.5k
views
DESeq2 on NanoString Data
deseq2
nanostring
updated 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
casey.rimland
▴ 150
1
vote
1
reply
1.1k
views
DESeq2 confounding cartridge
deseq2
confounders
nanostring
rnaseq
differential gene expression
updated 6.2 years ago by
Michael Love
42k • written 6.2 years ago by
kim.malek88
• 0
0
votes
0
replies
1.4k
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
3
votes
8
replies
3.4k
views
Using DESeq2 with Nanostring data (for VST only)
deseq2
variancestabilizingtransformation
nanostring
updated 7.1 years ago by
Michael Love
42k • written 7.1 years ago by
johnmcma
▴ 10
2
votes
0
replies
1.9k
views
NanoString Data Normalization Revisited
nanostring
normalization
8.6 years ago
alakatos
▴ 130
24
votes
12
replies
12k
views
Nanostring analysis with limma
nanostring
limma
updated 9.0 years ago by
ker61
▴ 20 • written 9.1 years ago by
mali salmon
▴ 370
18 results • Page
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Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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