Binning expression data along with capturing gene identifiers

alan_sm · 01-26-2015, 06:35 AM

Got the answer from Bioconductor support
Thanks to johannes.rainer
https://support.bioconductor.org/p/64409/#64433

Hello,

I'm using cut function to bin my expression data (FPKM) to know the
distribution of expression in different bins and plot them. However, it
won't capture gene identifiers of genes (row names) in different bins. I
wonder if there is any function in one of the CRAN or Bioconductor packages or any code to do so.

I use this for binning:
fpkmBins <-
table(cut(fpkm[,2],breaks=c(0,0.01,1,2,3,4,5,10,20,30,40,50,60,70,80,90,100,12000),dig.lab=5,include.lowest=TRUE,labels=c("0","<1","1-2","2-3","3-4","4-5","5-10","10-20","20-30","30-40","40-50","50-60","60-70","70-80","80-90","90-100",">100")))

Thanks in advance .
Alan

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01-26-2015, 06:35 AM	#1
alan_sm Junior Member Location: USA Join Date: Sep 2012 Posts: 3	Answered: Binning expression data along with capturing gene identifiers Got the answer from Bioconductor support Thanks to johannes.rainer https://support.bioconductor.org/p/64409/#64433 Hello, I'm using cut function to bin my expression data (FPKM) to know the distribution of expression in different bins and plot them. However, it won't capture gene identifiers of genes (row names) in different bins. I wonder if there is any function in one of the CRAN or Bioconductor packages or any code to do so. I use this for binning: fpkmBins <- table(cut(fpkm[,2],breaks=c(0,0.01,1,2,3,4,5,10,20,30,40,50,60,70,80,90,100,12000),dig.lab=5,include.lowest=TRUE,labels=c("0","<1","1-2","2-3","3-4","4-5","5-10","10-20","20-30","30-40","40-50","50-60","60-70","70-80","80-90","90-100",">100"))) Thanks in advance . Alan Last edited by alan_sm; 01-26-2015 at 09:34 AM. Reason: Got the answer from Bioconductor support