How do I determine p-value and fold change for TMM normalized data?
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13 days ago
Gof • 0

Hi,

I have a TMM normalized data for cancer vs no cancer treatment. This data, however, does not contain p-value or fold change. I want to generate plots such as heatmaps and volcano plots, but I cann't do it without their p-values and fold changes. I also do not have the raw counts. Is there a way to calculate p-value and fold change for this normalized data. Any help is greatly appreciated.

Thanks.

TMM P-value normalization • 186 views
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There might be a way to get fold changes from this kind of data in limma.

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12 days ago
ATpoint 54k

This discusses the options, by the way, this has been dozens of times before, please use the search function and google, or point out why none of the previous threads was able to help.

https://support.bioconductor.org/p/125144/#125156

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