Comments (10)
https://cptac-data-portal.georgetown.edu/study-summary/S046
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@mcreixell have you looked into this? If not I was thinking of doing some exploring about how to start this analysis...
from ddmc.
Yes, I'm currently working on this.
from ddmc.
Ok great.
from ddmc.
It looks to me like the data is under the phosphoproteome
folders here:
https://cptc-xfer.uis.georgetown.edu/publicData/Phase_III_Data/CPTAC_LUAD_S046/
You then go into the *PSM
folder, then *.tsv
folder, then all the files inside have the relevant data. Seems like a ton.
from ddmc.
Hmm... actually, not sure I see the location assignment within the protein. Must be around somewhere, though.
from ddmc.
Yes, the number at the beginning of each file name (1-25) indicates the TMT10-plex experiment. Within each experiment, 8 are tumor-normal pairs, one is an internal reference (tumor or normal only), and the 10th is a pooled reference sample. I think all these files are integrated in the file I sent in my email via google drive.
from ddmc.
Aha, I see now.
from ddmc.
The model seems to work. It's been running for ~2h and still active. How would you deal with the fact that the dataset contains tumor and healthy peptide signal for each patient? Would you model the entire data set as it is or maybe normalize to healthy?
from ddmc.
Wonderful! Might try profiling as the slow spots could be different. I'd suggest ignoring the healthy/normal labels for now and looking at them after clustering.
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Related Issues (20)
- Methods manuscript layout HOT 1
- Update Shuffle figure
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- Describe Fixed PAM250 method in manuscript HOT 2
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- Word document export error HOT 2
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- Discuss GSEA plots
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