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hamiltonoh / organage

A package to estimate biological organ age using SomaScan plasma proteomics data
MIT License
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error of no protein for many organs #3

Open khomicsk opened 8 months ago

khomicsk commented 8 months ago

Dear all,

Thanks for the development of this nice tool. We ran it on our dataset of serum samples analyzed with SomaLogic v4.1 data in 130 patients.

We did get results but also many of the organ-specific prediction fail to work and receive the following message:

"there are no proteins for a lot of the organs, it only works on heart, kidney,muscle , cognition liver, cognition kidney, cognition muscle, cognition immune, cognition heart"

can you explain the reasons or what might have been done incorrectly.

We used the RFU data obtained by the readat pipeline with the function getIntensities

Thanks

K

hamiltonoh commented 8 months ago

Hi K,

This means that those organ-specific proteins are missing from your dataframe. Make sure you have all the SeqIds that are needed. Maybe some are missing because they are not detected in serum (we use plasma)?

Best, Hamilton

khomicsk commented 8 months ago

Dear Hamilton

Thanks for taking the time to answer.

I do not think that the serum/plasma difference is the answer.

I checked manually the proteins as per your supplementary table 5 (ST5) for the conventional signature. All proteins seemed to be expressed in my data, and the SeqIDs were correct as well.

Any other suggestions?

Thanks

Happy holidays

K