I am new to Synapse and would like to use microRNA-seq expression data from the KIRC project. I would like to find out, whether and, if so, how the raw data were treated to end up in the format they are, e.g. in syn1445812. Thank you so much for your consideration and time. Andreas
Created by Andreas Scherer Scherer Thank you all very much.
Gordon, looking at your publication clarifies my question. So the data matrix is ready for analysis e.g. in limma.
Best regards,
Andreas Andreas, have you looked at the NAR publication? If this does not give you what you need, please email me (Gordon Robertson) -
Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Large-scale profiling of microRNAs for The Cancer Genome Atlas. Nucleic Acids Res. 2016 Jan 8;44(1):e3. doi: 10.1093/nar/gkv808. Epub 2015 Aug 13. PMID: 26271990 Hi Andreas:
You can also follow the provenance for this file (available from the bottom right of the page and inserted below). Provenance links back to the input files that were used to create this file. For this specific file the data was imported from the TCGA DCC that has been retired since the file was imported so are not available anymore.
${provenance?entityList=syn1445812&depth=2&showExpand=false}
Best,
Larsson Hi @Scherer!
Welcome to Synapse! Your best bet for learning more about specific files/data, other than reading the wiki page for that file, is by either asking the owner of the file (in this case, it's @kellrott) or by asking this same question in the discussion forum for the project, which can be found here: https://www.synapse.org/#!Synapse:syn300013/discussion/ It's possible other Synapse users may know as well -- I'll let my colleagues know about this thread and see if they have better advice.
Thanks!
-Meredith
Drop files to upload
KIRC microRNA expression data: preprocessing scheme page is loading…