Bioconductor Confounders

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scRNA-seq MAST confounders

updated 5.3 years ago by Andrew_McDavid ▴ 280 • written 5.3 years ago by ramonmassoni ▴ 10

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limma limma-voom limma design matrix confounders

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by S.Bamopoulos ▴ 10

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deseq2 confounders nanostring rnaseq differential gene expression

updated 7.1 years ago by Michael Love 43k • written 7.1 years ago by kim.malek88 • 0

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ruvseq deseq2 model.matrix confounders

updated 7.7 years ago by davide risso ▴ 980 • written 7.7 years ago by heikki.sarin ▴ 10

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deseq2 confounders design matrix rnaseq

8.0 years ago lina.faller ▴ 10

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minfi bumphunter confounders

updated 8.1 years ago by James W. MacDonald 68k • written 8.1 years ago by gft219 • 0

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edgeR paired samples confounders model.matrix

updated 8.8 years ago by Ryan C. Thompson ★ 7.9k • written 8.8 years ago by manasishah86 ▴ 30

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deseq2 rnaseq_analysis variancestabilizingtransformation confounders

updated 8.9 years ago by Michael Love 43k • written 8.9 years ago by ompandey ▴ 10

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Deseq2 dds confounders

updated 9.3 years ago by Michael Love 43k • written 9.3 years ago by colaneri ▴ 30

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Comment: error in ChAMP loading file by janwilseo • 0

Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…

Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0

One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…

Comment: DESeq2 Design controlling for gender by donnycrimson • 0

On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…

Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0

Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …

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remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline

How to remove X & Y chromosome genes from RNAseq data

Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?

A: Unbalanced experiment with multiple samples from each patient.

A: Understanding contrasts limma

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