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kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
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the id transversion maybe not ftit for all counts matrix #59

Closed dj10086 closed 4 years ago

dj10086 commented 4 years ago

ens <- rownames(airway)

library(org.Hs.eg.db) symbols <- mapIds(org.Hs.eg.db, keys = ens, column = c('SYMBOL'), keytype = 'ENSEMBL') symbols <- symbols[!is.na(symbols)] symbols <- symbols[match(rownames(airway), names(symbols))] ens <- rownames(airway)

library(org.Hs.eg.db) symbols <- mapIds(org.Hs.eg.db, keys = ens, column = c('SYMBOL'), keytype = 'ENSEMBL') symbols <- symbols[!is.na(symbols)] symbols <- symbols[match(rownames(airway), names(symbols))] rownames(airway) <- symbols keep <- !is.na(rownames(airway)) airway <- airway[keep,] keep <- !is.na(rownames(airway)) airway <- airway[keep,]

use this code in my own data, it report error, Error in .rowNamesDF<-(x, value = value) : mo 'row.names' deplicated permitted thanks a lot

kevinblighe commented 4 years ago

It seems that you have not actually used any EnhancedVolcano function here (?). The error appears to relate to duplicate rownames in one of your data-frames

dj10086 commented 4 years ago

I haved used. I tested all the code in this, here is just one error. thanks a lot, I also want you to revise the rna-seq script more robust whenyou are not busy. image

kevinblighe commented 4 years ago

Hi, to solve this new error, you need to install the version from GitHub. These new changes have not yet been released, officially.

You can try: remotes::install_github('kevinblighe/EnhancedVolcano')

dj10086 commented 4 years ago

thanks a lot, I willtry now I also want you to revise the rna-seq script more robust when you are not busy

kevinblighe commented 4 years ago

If you need help with other things, perhaps you can create a question on Biostars?