Bioconductor Expression

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969

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expression R filtering limma

8 months ago • updated 6 months ago mohammedtoufiq91 ▴ 10

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203

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expression variancePartition edgeR

9 months ago Jonathan • 0

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773

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microarray quantile expression R Normalization

updated 22 months ago by Konstantinos Yeles ▴ 80 • written 23 months ago by mohammedtoufiq91 ▴ 10

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744

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GEO expression GEOquery

updated 3.1 years ago by Robert Castelo ★ 3.0k • written 3.1 years ago by lsbew • 0

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1.2k

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RATs RNA-Seq Isoforms DTU expression

updated 3.9 years ago by fruce_ki ▴ 20 • written 3.9 years ago by UserAnonyme • 0

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497

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deseq2 genes expression

updated 4.2 years ago by Michael Love 40k • written 4.2 years ago by UserAnonyme • 0

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2.4k

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rpkm scater calcaverage R expression

updated 4.2 years ago by Aaron Lun ★ 28k • written 4.2 years ago by kushshah ▴ 10

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976

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variance formula expression

updated 4.4 years ago by mikhael.manurung ▴ 270 • written 4.4 years ago by rina ▴ 20

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1.4k

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job sequencing methylation expression Job

8.3 years ago Andy Lynch ▴ 120

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1.5k

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ebayes expression affymetrix pd.hugene.2.0.st limma

updated 8.4 years ago by Gordon Smyth 47k • written 8.4 years ago by Paulo Nuin ▴ 200

10 results • Page 1 of 1

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Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k

I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…

Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k

Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k

> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…

Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k

Yes, with normalized counts on log2 scale.

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20

A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…

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A: Ranges from a fasta file

Answer: NA transcript values in my Txdb

Comment: Interpret plot from DiffBind

Answer: Use with_go along with other filters in getBM function

Awards • All

Scholar to Mike Smith ★ 6.0k