Showing : confounders • reset
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comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 2.4 years ago by ▴ 260 • written 2.4 years ago by ▴ 10
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6
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Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma limma-voom limma design matrix confounders
updated 3.9 years ago by ★ 27k • written 3.9 years ago by ▴ 10
1
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674
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 4.2 years ago by 37k • written 4.2 years ago by • 0
0
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1
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1.5k
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RUVseq: How to implement to more complex time-course model?
ruvseq deseq2 model.matrix confounders
updated 4.8 years ago by ▴ 890 • written 4.8 years ago by ▴ 10
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7
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DESeq2: how to identify confounding variable in the design matrix
deseq2 confounders design matrix rnaseq
5.1 years ago lina.faller • 0
0
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3
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Controlling for confounding variables in bumphunter
minfi bumphunter confounders
updated 5.2 years ago by 59k • written 5.2 years ago by • 0
2
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11
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1.1k
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Adjusting for confounders along with paired testing using edgeR
edgeR paired samples confounders model.matrix
updated 5.9 years ago by 7.8k • written 5.9 years ago by ▴ 30
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3
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How to do a confounding variable adjustment without using the treatment information?
deseq2 rnaseq_analysis variancestabilizingtransformation confounders
updated 6.0 years ago by 37k • written 6.0 years ago by • 0
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5
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how to design a formula in DEseq2 that control for the effect of putative confounders?
Deseq2 dds confounders
updated 6.4 years ago by 37k • written 6.4 years ago by ▴ 30
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Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI() by shepherl 3.1k
I'm not able to reproduce this. Maybe it was a temporary issue with biomaRt? ``` > makeOrgPackageFromNCBI( + version = "0.1", + …
Comment: CPM after RUVseq by Jess • 0
Ah I think I know where the communication breakdown is occurring. When I think of RUVr, I'm including fitting the preliminary model in edge…
Answer: NMF installation with current R version by shepherl 3.1k
Install the Biobase package ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::ins…
Answer: Creating DESeq object and choosing a contrast by Michael Love 37k
If you've read over the section on interactions and are still confused what these terms mean, I'd recommend consulting with a statistician …
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa by Michael Love 37k
hi, Good question. So you can aggregate your swish isoform results to gene level (for which genes are there any significant isoforms) and …
Votes
A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
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