Question: GSVA with NanoString nCounter data
gravatar for SB
10 months ago by
United States
SB0 wrote:

Dear Bioconductors, 

I am quite new to bioinformatics analysis and am interested in using the GSVA function with NanoString nCounter Data. I have read that "the NanoString nCounter is most similar to RNA-Seq in that it processes discrete counts of measurement similar to RNA-Seq." Thus, I was under the impression that when inputting the NanoString data into GSVA, I would treat it like RNAseq data. Is this a reasonable assumption? 



gsva nanostring • 225 views
ADD COMMENTlink modified 7 weeks ago • written 10 months ago by SB0
Answer: GSVA with NanoString nCounter Data - Pre-Processing
gravatar for Robert Castelo
10 months ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:


i have no experience with NanoString nCounter data so i cannot give you an specific advice in using GSVA with this technology. GSVA does not perform any normalization of the data and it is the responsibility of the user to provide data normalized to the 'gsva()' function. Normalizing data essentially means to make molecular measurements comparable across samples. You should follow the recommended steps to normalize Nanostring nCounter data. If the resulting normalized data are continuous values then you can call the 'gsva()' function with the default argument kcdf="Gaussian". If the resulting normalized data are discrete integer count values then you should call the 'gsva()' function with the argument kcdf="Poisson".

hope it helps,


ADD COMMENTlink written 10 months ago by Robert Castelo2.3k
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