Question

Adding Phenodata after processing in Lumi

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Marino, Rebecca Bosko ▴ 10

@marino-rebecca-bosko-4774

Last seen 9.6 years ago

Hi List, Does anyone know if it is possible to add phenoData into lumi after you process your samples rather than during import with lumiR.batch? We have close to 500 samples in 4 batches of 96 and I'm currently finding myself wanting to add or update phenoData after the import. As importing such large scale batches are taxing on my processor, it would be much easier to import the data/phenoData and be able to update the phenoData later rather than having to re-import when I decide to add another variable to the phenoData. I'm relatively new to R, bioconductor, and lumi so I don't know if there is a well known method to do this that I'm currently unfamiliar with. Any help would be much appreciated. Thanks for any Advice, Becky Marino [[alternative HTML version deleted]]

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ADD COMMENT • link updated 9.1 years ago by Chi Hong • 0 • written 12.8 years ago by Marino, Rebecca Bosko ▴ 10

score 0 · Answer 1 · 2015-03-05

See if this helps:

Adding a column to phenoData dataframe

In addition, if you have a separate phenotype file that you'd like to add, you do something like:

pData(lumiBatch.object) = phenotype.file

or

pData(lumiBatch.object) = merge( x=pData(lumiBatch.object), y=phenotype.file, by.x="sampleID", by.x="ID.in.phenotype.file", all=TRUE)