Flooring (adjusting) values in Gene Expression Microarray data analysis?

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2.9 years ago

mohammedtoufiq91 ▴ 250

Hi,

I am analysing large datasets in R, and came across an issue. There are some values less than 10 in the dataset and I would like to floor/adjust the values to (=10). I usually floor the values (=10) at the probe-level data > Normalize the data > then convert the data from probe-level to gene-level data by matching with Gene Symbols. I have a question, does adjusting operation makes sense for data at probe-level or gene-level? or do, you think it's OK at any level?

data.matrix[data.matrix<10]=10

Thank you,

Toufiq

gene-expression microarray R • 492 views

ADD COMMENT • link updated 2.9 years ago by ATpoint 81k • written 2.9 years ago by mohammedtoufiq91 ▴ 250

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Arbitrary altering data is usually not recommended. Be sure to follow standard pipelines such as outlined in the limma manual for microarrays.

ADD REPLY • link 2.9 years ago by ATpoint 81k

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