limma: Camera() about the input data
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django_w • 0
@django_w-14010
Last seen 3.8 years ago

I download the cancer gene expression data from TCGA repository as the input data of CAMERA function in package 'limma'. however, i have some confusion about the data preprocessing. 

I downloaded normalized data and process it using log function. Then, the problem is coming, I want to ask whether can I process the data using Z-score function after the previous step. as the input of CAMERA function.

limma camera • 831 views
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@gordon-smyth
Last seen 57 minutes ago
WEHI, Melbourne, Australia

In general, camera() can be run on log-expression data, as would be used for any differential expression analysis.

I can't comment specifically on data that you may have downloaded from the TCGA. I don't know what you mean by a "Z-score function" but it doesn't sound like anything you would need or want to apply to already normalised data.

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