Showing : confounders • reset
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comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.8 years ago by ▴ 280 • written 5.8 years ago by ▴ 10
2
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6
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2.2k
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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 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 10
1
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1
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.5 years ago by 43k • written 7.6 years ago by • 0
0
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1
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2.7k
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RUVseq: How to implement to more complex time-course model?
ruvseq deseq2 model.matrix confounders
updated 8.2 years ago by ▴ 980 • written 8.2 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
8.5 years ago lina.faller ▴ 10
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3
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Controlling for confounding variables in bumphunter
minfi bumphunter confounders
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
2
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11
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Adjusting for confounders along with paired testing using edgeR
edgeR paired samples confounders model.matrix
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 30
4
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How to do a confounding variable adjustment without using the treatment information?
deseq2 rnaseq_analysis variancestabilizingtransformation confounders
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 10
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how to design a formula in DEseq2 that control for the effect of putative confounders?
Deseq2 dds confounders
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 30
9 results • Page 1 of 1
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Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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