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
2.2 years ago Zhijie • 0
0
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3
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2.8k
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[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet Assay NanoString Error Data
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
2
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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 3.1 years ago by 43k • written 3.1 years ago by • 0
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5
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2.2k
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how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 7 months ago by ▴ 70 • written 3.7 years ago by ▴ 50
3
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6
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2.3k
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Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 16 months ago by • 0 • written 5.6 years ago by ▴ 50
0
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1
reply
2.0k
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Application of RUV to a small Nanostring dataset
RUV Nanostring RUV-III
updated 4.9 years ago by ▴ 20 • written 5.6 years ago by ▴ 30
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9
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1.9k
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DESeq2 with nanostring data
deseq2 nanostring
5.2 years ago acs1990 ▴ 10
0
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4
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1.3k
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Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.4 years ago by 52k • written 5.4 years ago by • 0
16
votes
40
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Can NanoString data be analyzed using DESeq2?
NanoString Differential Expressed Genes Analysis DESeq2
updated 3.2 years ago by ▴ 10 • written 5.6 years ago by ▴ 50
1
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1
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1.8k
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GSVA with NanoString nCounter data
GSVA Nanostring
6.6 years ago • updated 5.9 years ago SB • 0
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5
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1.6k
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NanoStringDiff analysis with confounding factors
differential gene expression nanostring confounding factors
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
1
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6
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2.4k
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How to access normalized data in the NanoStringDiff package?
nanostringdiff nanostring NanoStringDiff
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 170
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13
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6.6k
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DESeq2 on NanoString Data
deseq2 nanostring
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 170
1
vote
1
reply
1.3k
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
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1.6k
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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
7.6 years ago c.kohler • 0
3
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8
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3.9k
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Using DESeq2 with Nanostring data (for VST only)
deseq2 variancestabilizingtransformation nanostring
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
2
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0
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2.1k
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NanoString Data Normalization Revisited
nanostring normalization
9.4 years ago alakatos ▴ 130
24
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12
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13k
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Nanostring analysis with limma
nanostring limma
updated 9.8 years ago by ▴ 20 • written 9.9 years ago by ▴ 370
18 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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