Bioconductor Filtering on probe annotation

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illumina human ht-12 v4 illuminahumanv4.db filtering on probe annotation illumina

updated 9.7 years ago by Mike Smith ★ 6.6k • written 9.7 years ago by svlachavas ▴ 840

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Answer: accounting for vs. removing batch effects with DESeq2 in RNAseq analysis by ATpoint ★ 4.6k

The vignette covers batch effects as per the authors best practice, please read it and consider following it.

Comment: DESeq2 analysis with transcript counts by kahunroleh • 0

Thanks for sharing the solution. I also face this problem. [nulls][1] [1]: https://nulls-brawl-apk.fr/

Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by kahunroleh • 0

Yes, you can perform DEG analysis across two batches with one shared sample by using batch correction methods like ComBat or limma. These t…

Comment: displaying the differential expression with deseq2 over 4X2 samples with the in by Martijn • 0

thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…

Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0

Thank you, this does clarify the available options.

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