Question: TCGA controlled data
gravatar for ugandhar.ch1
4 days ago by
ugandhar.ch10 wrote:

Hi All,

i am using R and Bio conductor for analyzing TCGA controlled data BRCA. 

data category raw microarray

data type raw intensities

platform Affymetrix SNP Array 6.0

access controlled

i used commands tcgabiolinks

i used command GDC query

GDC download(query)

GDC prepare

i am not sure what should i do after this step?

my final aim to do differential expression?

what  package should i use?

what prompt i get after GDC prepare? i think i should get expression set, but i am not getting it

tcga data is downloaded and placed in working directory


please help me.. i am not finding any source for help


Thank You



ADD COMMENTlink modified 4 days ago • written 4 days ago by ugandhar.ch10

If you are intending to get data from the Affy SNP 6.0 array, you should note that this is genotype data, not expression data. So if you want to do differential expression you need a different array platform.

ADD REPLYlink written 4 days ago by James W. MacDonald43k
gravatar for ugandhar.ch1
4 days ago by
ugandhar.ch10 wrote:

hi James,

thank you for your reply. which package should i use? can you please tell me

i am really struggling with it


Thank You


ADD COMMENTlink written 4 days ago by ugandhar.ch10

If you have a followup question, use the ADD REPLY button and type in the box that comes up. The box below that says 'Add your answer' is for answers, not questions.

You don't have a specific question that can be easily answered, nor do you have any code that you tried that didn't work. If you want to use TCGA stuff, then I would use the RTCGAToolbox, which has a vignette you could read.

The nice thing about R and Bioconductor is that you get cutting edge software for free. The not so nice thing is that nothing in life is free. In this case you have to pay with the time you spend learning how to use R and the Bioc packages that you want to use. While the people on this support forum are helpful, and are willing to give advice, you cannot expect that they will give enough advice for you to be able to do what you want to do. For that you will need to read. And read some more. And use google to answer questions. If you want to use Open Source tools, there is no other way but to read and learn for yourself.


ADD REPLYlink written 3 days ago by James W. MacDonald43k
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