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1 day ago
jain72744
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10
Any tutorial on CPTAC proteomics data analysis. I am uncertain as to which files need to be downloaded and want to perform differential expression analysis?
Hi,
your previous questions have little to no responses and, importantly, all have little to no effort from your side. Please consider asking more elaborate questions indicating what you tried and a specific (not broad) question. There are many tutorials on proteomics on the one hand, and you do not show which files are available on the other hand. People will usually not first visit CPTAC to find out what they have available only to answer here, you need to provide the necessary information yourself.
Considering your suggestion, I'd like to elaborate what I wish to find. I started with proteomics analysis form TCGA data obtaining the proteomic profiling for TCGA-LIHC using the R code : query_protein<- GDCquery(project="TCGA-LIHC", data.category="Proteome Profiling", data.type="Protein Expression Quantification", experimental.strategy='Reverse Phase Protein Array'). I wished to find differentially expressed proteins and further relate them to my DEGs. However, this data was limited to only tumor samples which made finding the differential expression impossible.
After this, I came across CPTAC portal containing PDC data where I found the study PDC000198 for HCC. Now I am unsure as to work with raw files, processed data and all other kind of files to fulfil my purpose of identifying Differentially expressed proteins (DEPs). Therefore, I wished to find any tutorial which can guide me for the same since different R packages for DEP analysis require differently processed data. I figures I will perform limma based analysis but again , due to scattered information, I am not sure if I am going in the right direction.
Please note also that there are also forums that directly relate to CPTAC (only), which may be more appropriate depending on the nature of your question.
For me, if my question is: "I have this data (that just so happens to be from CPTAC but in principle could have been any data of this type) and I want to (do this bioinformatic task)" --> I would pick Biostars.
However, if my question is about CPTAC-specific files/organization/folder structure/artifacts/etc --> I would ask in a dedicated CPTAC forum.