Biomarkers Consortium Plasma Proteomics

[Juliana Nery de Souza Talarico]

Hi Danielle,

I’m analyzing data from the Biomarkers Consortium Plasma Proteomics Project RBM Multiplex Data and Primer dataset and it sounds that the analytes values

were transformed (i.e., to have normal distribution). I read the protocol but could not find a precise information about it. Can you please if the variables or transformed and what kind of transformation was used (e.g., log, z-scores, centered, etc.)?

Thank you

Juliana

 

[Danielle J Harvey]

Hi Juliana,

 

My apologies for the delay in responding – I was out of the office for several days and am just now catching up on emails. These are data submitted by a consortium that requested samples from ADNI, so the only information I have about the data is what you can see in the associated methods documents that are included in the zip file you download from LONI (if you click to download the Biomarkers Consortium Plasma Proteomics Project RBM Multiplex Data and Primer). In the methods document are email addresses for contacts if there are additional queries about the data, so I’d recommend contacting one of those individuals.

 

Danielle

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[Juliana Nery de Souza Talarico]

Sounds good! I’ll contact them. Thank you so much, Danielle!

Have a great day!
Juliana

 

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[Dave E]

Hi Juliana,

I don't know if this helps, but there's a column in the *raw* plasma data indicating if a Log Transform has been used or not (1 or 0). 

I have had only a quick look, but a 0 matches either the raw untransformed value ('as-is') has been used in the QC data, or that the raw value falls outside the QC range (and presumably dropped - I haven't checked).  The *raw* data file also shows before and after log transformed values (or as-is, as appropriate) in the Analysis Value column. 

The protocol document is a bit misleading as it sort of implies anything goes, but then mentions only Box-Cox specifically.

So TL:DR - it seems the values are as-is; or log10; or dropped.

Not an expert BTW, but I have dabbled a few times.....

HTH,

Dave

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