Are there any methods to perform the proteome profiling of GDC TCGA through R programming and to connect it with the gene expression profiling results ?
@Zhenyu Zhang, can I get some insights on this query ??
assuming most GDC R packages such as tcgabiolinks or genomicsdatacommons can do it. you are also get the data directly from the gdc data portal
Dear Sir, I have curated the data but I am not able to perform proteome expression profiling as I am confused with RPPA format data, which is present on TCGA. Eventhough paper on this are very less. Threfore, May I get some insights on the codes which can be used from R packages to perform the RPPA format proteome expression profiling of the patient samples from tcga on R?
I don't know what exactly you want.
They are TSV files, and by code, are you asking for read.table()?
I don't know what you are asking about "connect to gene expression"? Are you trying to look for data from the same aliquot, or are your trying to do correlation analysis?
Hi, Thanks for reply after so long. I will be doing some correlation or integrative analysis of both gene and protein data. Therefore, before that I am thinking to do the proteome expression profiling of the proteome data which is on TCGA. Hence, Is this correct to do the proteome expression analysis by using the edge R package ? or Is there any other way of doing it? please let me know. Since the proteome data on TCGA is in RPPA format and I am confused "how to analyse this?"
Any guidance would be grateful for me move forward in my work.
The RPPA data have been normalized and probably batch corrected. In general, I would suggest you using generate statistics method such as correlation/linear regression, etc instead of regular RNA-Seq analysis tools. But I am not an expert in this area. I remember there was a major CPTAC-3 paper published either this year or last year, and that should be a reference paper for cancer proteomics analysis.
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For the non-cancer biologists confused by esoteric acronyms, GDC stands for Genomic Data Commons, and represents a data portal whereby one can retrieve various cancer data sets collected under the Cancer Genome Atlas Program (TCGA) which was initiated several years ago. @qiz18591 it would be very helpful to add even a small amount of information to your question that could inform curious biologists to know what your question is about. e.g. "I'm interested in comparing proteome and transcriptome profiles across cancer data sets..."
Sorry but this reply isnt the answer of my question. I have read about TCGA, transcriptome profiling,etc but I am not able to figure about the proteome profiling. And this is true, I am interested in comparing proteome and trasncriptome profiles across datasets. Do you have tutorial codes to share on this???
Of course it's not the answer to your question. If I had intended to answer your question, I would have put the answer in the answer section. Rather this was simply a comment to you about your question that in the future you might try to make it more readable and understandable to more people by explaining your general intent, giving context, and explaining your acronyms. I know a fair amount about proteomics, transcription, and R, and yet I was unable to understand your question when I first saw it. Now that I do understand it, I don't have any code you would find useful, but would simply have to hack around myself.
Thank you