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8.6 years ago
Harry_Potter
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0
Do both tools offer the same information? Which one is easier to use with R, and can you get different info from them in R?
To answer your specific question, try http://www.cbioportal.org/ - it has useful utilities for extracting RNA-seq data from TCGA.
More broadly, you may find this post from someone that was in your shoes quite helpful: C: [UPDATE] Thrown into a Bioinformatics Position
PS, don't work in Excel. Learn R.
Thanks so much! That was super inspiring and really appreciated. I spent the day on excel with fire browse data. Yesterday evening
sorry, that sent before I meant it to. Yesterday evening, I was trying to utilize cbioportal in R. I'll get there, slowly but surely.
1) a little of google search brings you a long way 2) what do you want to do with the data? 3) can you code in R? if so that's the way to go 4) if you cannot code in R for basic questions use cBioportal as suggested 5) for single gene expression across tumors you can also check firebrowse
Thanks so much!!
OK, so I still am not understanding "normalized" expression data from plain old "gene_expression" in firebrowse. What do they mean by normalized?
And which one involves the log2 conversion?
Hi Harry_Potter,
Shame that you get thrown into this project without adequate support. Your questions mainly depend on what you aim to achieve in your analysis. What is your background? Do you have any experience with this kind of work?
I have a wet lab background and want to get into bioinformatics because I think the data is so compelling, especially with cancer research. You can get around the issues with immortalized cell lines that are far different than their original source. Don't get me wrong, molecular biology is great to confirm hypotheses.
Unfortunately, I have no background in bioinformatics. I figured as a graduate student, I am here to learn, so why not pursue something that I am interested in. I thought I would have a teacher or guide, but clearly I am not going to. Still, I am determined to make it work.
I suggest you start of with following a few tutorials on this and read papers in which people do similar things as you want to achieve.