CPTAC RData share - Githubissues

miccec / MAKINA

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CPTAC RData share #1

Open changwenwang09 opened 1 year ago

changwenwang09 commented 1 year ago

I am quite interested in the method and would like to repeat the analysis to further understand it. I found the normalized CPTAC data from the original publication, but I am not sure whether that was what you had as input.

Would it be possible for you to share the CPTAC_GBM_proteomics.RData and the CPTAC_GBM_phosphoProteomics.RData so I know how the input data was constructed?

Thanks a lot!

lucgar commented 1 year ago

Hello, I also used the normalized CPTAC data from the original publication. I'm not sure I can include the files on the repository, as their size is big, but I'll try. Anyhow, here is how the input files should be:

CPTAC_GBM_proteomics.RData, includes a matrix called Proteome with the proteins in the rows and the samples in the columns;
CPTAC_GBM_phosphoProteomics.RData, includes 2 objects, a matrix called Phospho_Proteome with the phosphorites in the rows and the samples in the columns, and a data.frame called Phospho_Proteome_fData that I derived from their matrix in which there are informations about each sites like the attached screen shot.

changwenwang09 commented 1 year ago

Thanks a lot for the reply! Maybe you could share a dropbox or other cloud download link or so? I can also try to construct as what you did if not possible :)

changwenwang09 commented 1 year ago

While trying to generate the data you described above, I noticed that you might have done filtering or averaging steps since there are some duplicated proteins in the proteome data set, and several phospho-sites were also not present in your data. It would be really helpful if you share the code of how you generated the data sets, and what your standards would be. Thanks a lot!

cerencuzun commented 1 year ago

Hello @lucgar, I am also trying to replicate the study with the code you have provided. The algorithm will be very useful for my own research. Is it possible to share the CPTAC_GBM_proteomics.RData and the CPTAC_GBM_phosphoProteomics.RData via Drive or Dropbox links? Or as @changwenwang09 stated above, if you can share the workflow of the generation of the datasets, that would be so helpful. Thanks is advance!