Bioconductor Log-linear

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RNA-seq Log-linear Main effects

updated 8.2 years ago by Aaron Lun ★ 28k • written 8.2 years ago by natalia.fghf • 0

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Comment: lfcShrink and alpha value by cropero • 0

Thank you so much! Would that be equivalent to perform `res <- results(dds, contrast = c("conditions", "wild_type_114_2_no_carbon", "wild_t…

Comment: pathview - multiple states by Philippine • 0

Thank you! Here a subset of genes that really works with "ame04145". data <- data.frame( EntrezID = c(100577548, 100577764, 406…

Comment: pathview - multiple states by Guido Hooiveld ★ 4.1k

A quick comment after I copied/pasted your code: when using `geneList1` in the 3rd code chunk I do **not** get a nice plot... I rather got …

Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Adam • 0

Hi Aaron, Thanks a lot for your help! As you mentioned, I checked my data and it is "DelayedMatrix". I don't know the detailed differe…

Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…

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