Bioconductor Diagnostic plots

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deseq2 diagnostic plots

updated 6.0 years ago by Michael Love 43k • written 6.0 years ago by Nancy ▴ 10

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limma custom diagnostic plots single

updated 9.2 years ago by Gordon Smyth 51k • written 9.2 years ago by dario.veneziano • 0

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limma multifactorial design diagnostic plots affymetrix microarrays

updated 9.2 years ago by James W. MacDonald 67k • written 9.2 years ago by svlachavas ▴ 840

3 results • Page 1 of 1

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Comment: Struggle with the replicates of epic array data by Melisa Tecik • 0

Thanks you so much for the instructions. I also tried M values as you suggested but sadly the result was the same. Apparently, the problem …

Answer: bioconductor packages on bioconda by James W. MacDonald 67k

The bioconda people are responsible for bioconda, so you should ask them if/when they are going to update.

Answer: txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome by James W. MacDonald 67k

The default for `plotKaryotype` is to use hg19.

Comment: Is it possible to parallelise saveHDF5SummarizedExperiment by Stefano Mangiola ▴ 20

saveTileDBSummarizedExperiment would be awesome. I think we need performance for execution time and memory required to save.

Comment: Create Illmina bead summary data by Liu • 0

Hi! Yes, thank you! I completely agree. I am just curious about how these two files are processed with AVG_Gre and detection p-value. I am …

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Answer: bioconductor packages on bioconda

Answer: Deseq2 res Function

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Scholar to James W. MacDonald 67k