Documentation states that brains were sampled at 4, 6, 12, and 24 months but here is the distribution of sampling dates I inferred from the difference between the date of birth and date of death:
```
JIP_APOE4.Trem2.R47H.sampInfo[!is.na(rnaID), inferred_sampling_date := difftime(mdy(dateDeath), mdy(dateBirth), units = 'days'), ]
ggplot(mapping = aes(inferred_sampling_date / 7 / 4), data = JIP_APOE4.Trem2.R47H.sampInfo[!is.na(rnaID), ]) + geom_freqpoly() +
scale_x_continuous(
breaks = c(0, 4, 6, 12, 24)
)
```
[Biospecimen sampling time histogram](https://drive.google.com/file/d/1VpDtnvr6p_XZ41DXGoGWNBCuMo-lFFf-/view?usp=sharing)
Thank you for your assistance!
Created by Rached Alkallas ralkallas Thanks again for all your help @annat22 and @ryaxley Hi @ralkallas
Indeed there is always some variation around the cohort age, in this dataset there was especially large variation for historical reasons. It is best to use the dates to infer age groups or range of age within age group as suits your needs. We will be updating the study description soon. Also, we will be updating the metadata as a whole soon, including genotype validation, so you might want to wait a bit.
If you have any other questions about this or any other jax model-ad dataset, feel free to contact me.
Best, Annat Thank you. I contacted the research team for clarification about the varied ages.
Rich Hi Ryan,
Thanks again for your responses.
I am not sure if you noticed the histogram I shared in the hyperlink in my initial post. In that histogram, I am plotting the difference between the date of birth and date of death of the mice from which brains were sampled. Presumably the date of death corresponds to the date of brain sampling.
I see four modes in the histogram. Only one mode is at 4 months but the other three modes deviate substantially from the study documentation which states that brains were sampled from mice at 4, 6, 12, and 24 months of age. The three modes deviate by about +2 to +3 months. I was hoping to understand why that is the case.
Thank you. Hi. @ralkallas
Would you please describe clearly what you have observed? What are the unexpected values?
Thanks,
Rich
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Jax.IU.Pitt_APOE4.Trem2.R47H (syn18345335) mouse brain sampling dates inconsistent with documentation page is loading…