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How to analyze whole ExpressionSet, instead of only example the first 1000 probes in phenoTest package using data( ) function?

Hi, I am using Bioconductor phenoTest package to analyze the data from GEO by getGEO. When I try to load these data using the data(eset), it only allows to load the first 1000 probes and 100 samples. How can I load all the probes (>20k) and samples (>100) for the following phenotype analysis?

Thank you!

Xiaoyong

r
• 1,878 views • link
updated by Ram Ram • written by xiaoyonf • xiaoyonf

Please post the commands you are using. Incidentally, data(eset) only loads an example dataset:

"For illustration purposes we selected the first 1000 genes and the first 100 samples, [...]"

Is any of your commands getGEO( something )?

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written by h.mon h.mon

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