normalize the SILAC light heavy value
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yueli7 ▴ 10
@yueli7-8401
Last seen 3 months ago
China

Hello,

I have SILAC protein data from three patients. How can I normalize the A10: Light/Heavy value over these patients?

Any available software or tools?

Thank you in advance for great help!

Best,

Yue

RforProteomics • 202 views
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@laurent-gatto-5645
Last seen 2 days ago
Belgium

I assume that when you mention 3 patients, you refer to 6 columns, 3 corresponding to the heavy and 3 to the light samples.

There's no special requirement to normalise such data. As always, it's advised to visualise your data (densities of the expression data, PCA, ...) before/after normalising to assess the effect of the transformation.

As for tools, you can consider MSnbase, DEP, ... or DAPAR, if you are less familiar with the command line interface.

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Hello Laurent Gatto, Laurent Gatto

Thank you so much for your quick response and great help!

I only has one column which has A10: Light/Heavy value. Please see the figure.

Is there any available R package or github software that can be use?

Thank you in advance for your great help!

Best,

Yue

Screen-Shot-2020-11-04-at-8-25-03-PM

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