Showing : NanoString • reset
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Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.2 years ago Zhijie • 0
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3
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3.5k
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[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet Assay NanoString Error Data
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
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3
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 4.1 years ago by 43k • written 4.2 years ago by • 0
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5
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how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 19 months ago by ▴ 70 • written 4.7 years ago by ▴ 60
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DESeq2 with nanostring data
deseq2 nanostring
6.2 years ago acs1990 ▴ 10
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4
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1.7k
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Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
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Application of RUV to a small Nanostring dataset
RUV Nanostring RUV-III
updated 5.9 years ago by ▴ 20 • written 6.6 years ago by ▴ 30
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6
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2.8k
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Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 2.4 years ago by • 0 • written 6.6 years ago by ▴ 60
17
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 6 months ago by 68k • written 6.6 years ago by ▴ 60
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5
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NanoStringDiff analysis with confounding factors
differential gene expression nanostring confounding factors
updated 7.2 years ago by 68k • written 7.2 years ago by • 0
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1
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2.2k
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GSVA with NanoString nCounter data
GSVA Nanostring
7.7 years ago • updated 7.0 years ago SB • 0
9
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15
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7.7k
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DESeq2 on NanoString Data
deseq2 nanostring
updated 6 months ago by 43k • written 7.8 years ago by ▴ 170
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6
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How to access normalized data in the NanoStringDiff package?
nanostringdiff nanostring NanoStringDiff
updated 7.8 years ago by 68k • written 7.8 years ago by ▴ 170
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1
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1.4k
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
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design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter
8.7 years ago c.kohler • 0
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8
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4.4k
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Using DESeq2 with Nanostring data (for VST only)
deseq2 variancestabilizingtransformation nanostring
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
2
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0
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2.4k
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NanoString Data Normalization Revisited
nanostring normalization
10.5 years ago alakatos ▴ 130
24
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12
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14k
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Nanostring analysis with limma
nanostring limma
updated 10.9 years ago by ▴ 20 • written 10.9 years ago by ▴ 370
18 results • Page 1 of 1
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Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label by nytwordlehints • 0
Amazing insights! I learned a lot from this.[pokemon overlord][1] [1]: https://pokemonoverlord.com
Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
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A: Fundamental questions about DESeq2 and RUVs in targeted gene set of 500
Answer: p-adjusted values in multiple comparisons
Comment: p-adjusted values in multiple comparisons
DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
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