To obtain excel expression file

Question

[djalminha_08]

Hi, I would like to obtain an excel file with normalized expression of rna (from rna-seq data) of all cases of one project (Paraganglioma) of TCGA (gdc now). I open the files with excel directly and the values of each transcript are strange, I think that I am doing something wrong.

I am new in Bioinformatics so I would apreciate simple answers. I learn fast.

Thank you very much.

Cheers!

[Pierre Lindenbaum]

[djalminha_08]

Ok, I could use R to process the data but I need export the RNA levels in a simplified format, like excel. I can learn R but other people in the laboratory needs something easier.

Thank you!

Cheers

[lieven.sterck]

and with simplified format you mean .xls I assume?

Can't think of a more simplified format than eg tab-delineated or csv ;-)

[WouterDeCoster]

Oh, some people struggle with a tab delimited file too. The struggles of a bioinformatician in a wet lab group...

Answer 1

[michael.ante]

Hi,

Please have a look at this paper Zeeberg et al. 2004. Not only automatical name interpretation, but also float to time conversions are usually made by Excel. An RPKM of 28.09 may be converted as the date 28th of September.

As an apprentice in Bioinformatics, you may want to learn R or Python for analyses of tables and matrices.

Cheers,

Michael

[lieven.sterck]

Fully agree!!

using "bioinformatics" and "excel" in a single sentence is just blasphemy :-) especially since I seem to read processing multiple files/list .

and a moderate amount of linux cmdline (or awk) will already get you a long way in tab file processing