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
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3
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2.9k
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[ExpressionSet] Question: Error in validObject(.Object)
ExpressionSet Assay NanoString Error Data
updated 2.7 years ago by 68k • written 2.7 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 3.2 years ago by 43k • written 3.2 years ago by • 0
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5
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2.3k
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how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 8 months ago by ▴ 70 • written 3.8 years ago by ▴ 60
3
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6
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2.4k
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Why NanoStringDiff package so slow?
NanoStringDiff NanoString nCounter DE analysis
updated 17 months ago by • 0 • written 5.7 years ago by ▴ 50
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1
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2.1k
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Application of RUV to a small Nanostring dataset
RUV Nanostring RUV-III
updated 4.9 years ago by ▴ 20 • written 5.7 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
5.3 years ago acs1990 ▴ 10
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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 5.5 years ago by 52k • written 5.5 years ago by • 0
16
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40
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11k
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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 5.7 years ago by ▴ 50
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1
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1.8k
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GSVA with NanoString nCounter data
GSVA Nanostring
6.7 years ago • updated 6.0 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 6.3 years ago by 68k • written 6.3 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 6.8 years ago by 68k • written 6.8 years ago by ▴ 170
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13
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6.7k
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DESeq2 on NanoString Data
deseq2 nanostring
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 170
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1
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1.3k
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.0 years ago by 43k • written 7.0 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
7.7 years ago c.kohler • 0
3
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8
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4.0k
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Using DESeq2 with Nanostring data (for VST only)
deseq2 variancestabilizingtransformation nanostring
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
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0
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2.2k
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NanoString Data Normalization Revisited
nanostring normalization
9.5 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 9.9 years ago by ▴ 20 • written 9.9 years ago by ▴ 370
18 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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