Question: To obtain excel expression file
0
gravatar for djalminha_08
8 months ago by
djalminha_0810
djalminha_0810 wrote:

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!

rna-seq expression • 403 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by djalminha_0810
6

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ADD REPLYlink written 8 months ago by Pierre Lindenbaum113k
1

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

ADD REPLYlink written 8 months ago by djalminha_0810

and with simplified format you mean .xls I assume?

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

ADD REPLYlink written 8 months ago by lieven.sterck2.6k
1

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

ADD REPLYlink written 8 months ago by WouterDeCoster32k
1
gravatar for michael.ante
8 months ago by
michael.ante2.7k
Austria/Vienna
michael.ante2.7k wrote:

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

ADD COMMENTlink written 8 months ago by michael.ante2.7k
1

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

ADD REPLYlink modified 8 months ago • written 8 months ago by lieven.sterck2.6k
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