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
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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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how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 7 months ago by ▴ 70 • written 3.8 years ago by ▴ 50
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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
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1
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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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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
16
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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
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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
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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
9
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13
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6.6k
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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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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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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
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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
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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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Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Comment: deseq2 lfc shrinkage with few DEGs by Michael Love 43k
Agree with your edit.
Votes
Comment: Using TPM from tximport of Salmon output for singscore
Answer: Using TPM from tximport of Salmon output for singscore
Comment: deseq2 lfc shrinkage with few DEGs
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
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