[R] calculating p-values by row for data frames

[Meyners, Michael, LAUSANNE, AppliedMathematics]

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Christoph Heuck
> Sent: Donnerstag, 15. Oktober 2009 17:51
> To: r-help at r-project.org
> Subject: [R] calculating p-values by row for data frames
> 
> Hello R-users,
> I am looking for an elegant way to calculate p-values for 
> each row of a data frame.
> My situation is as follows:
> I have a gene expression results from a microarray with 64 
> samples looking at 25626 genes. The results are in a data 
> frame with the dimensions 64 by 25626 I want to create a 
> volcano plot of difference of means vs. -log(10) of the 
> p-values, comparing normal samples to abnormal samples. The 
> results of both type of samples are all in my data frame.
> Now, I have found a way to calculate the p-value using a "for 
> (i in 1:25626)" loop (see below):
> 
> df.normal  #dataframe, which only contains the normal samples 
> df.samples  #dataframe, which only contains abnormal samples
> 
> DM=rowMeans(df.normal)-rowMeans(df.samples) #gives me a 
> dataframe with the difference of means
> 
> PV=array(1,c(25626,1))
> for (i in 1:25626){
> VL=t.test(matrix.b[i,],matrix.a[i,])
> V=as.numeric(VL[3])
> V=-log10(V)
> PV[i,1]=V}
> 
> plot(DM, PV, main=title,xlab=x.lab, ylab="-log(10) P-Values",pch=20)}
> 
> It takes around 3-5 minutes to generate the volcano plot this 
> way. I will be running arrays which will look at 2.2 million 
> sites >> this approach will then take way too long.
> I was wondering if there is a more elegant way to calculate 
> the p-values for an array/fataframe/matrix in a row-by row 
> fashion, which is similar to "rowMeans".
> 
> I thought writing a function to get the p-value and then using
> apply(x,1,function) would be the best.
> 
> I have the function which will give me the p-value
> 
> p.value = function (x,y){
> PV=as.numeric(t.test(x,y)[3])
> }
> 
> and I can get a result if I test it only on one row (below is 
> 6 by 10 data frame example of my original data)
> 
> RRR
>                      X259863    X267862     X267906    X300875
> X300877     X300878
> MSPI0406S00000183 -3.2257205 -3.2248899  2.85590082 -2.6293602
> -3.5054348 -2.62817269
> MSPI0406S00000238 -2.6661903 -3.1135020  2.17073881 -3.2357307
> -2.3309775 -1.76078452
> MSPI0406S00000239 -1.7636439 -0.6702877  0.19471126 -0.7397132
> -1.4332662 -0.24822470
> MSPI0406S00000300  0.6471381 -0.2638928 -0.61876054 -0.9180127
> 0.2539848 -0.63122203
> MSPI0406S00000301  0.9207208  0.2164267 -0.33238846 -1.1450717
> -0.2935584 -1.01659802
> MSPI0406S00000321 -0.4073272 -0.2852402 -0.08085746 -0.4109428
> -0.2185432 -0.39736137
> MSPI0406S00000352 -0.7074175 -0.6987548 -1.22004647 -0.8570551
> -0.5083861 -0.09267928
> MSPI0406S00000353 -0.2745682  0.3012990 -0.64787221 -0.5654195
> 0.4265007 -0.65963404
> MSPI0406S00000354 -1.1858394 -1.4388609 -0.07329722 -2.0010785
> -1.3245696 -1.43216984
> MSPI0406S00000360 -1.4599809 -1.4929059  0.63453235 -1.1476760
> -1.5849922 -1.03187399
> 
> > zz=p.value(RRR[1,1:3],RRR[1,4:6])
> > zz
> $p.value
> [1] 0.485727
> 
> but I cannot do this row by row using apply
> 
> > xxx=apply(RRR,1,p.value(RRR[,1:3],RRR[,4:6]))

xxx <- apply(RRR, 1, function(x) p.value(x[1:3],x[4:6]))
works for me. Check the examples in ?apply.
HTH, Michael

> 
> Error in match.fun(FUN) :
>   'p.value(RRR[, 1:3], RRR[, 4:6])' is not a function, 
> character or symbol
> 
> Does anyone have any suggestions?
> Thanks in advance
> 
> Christoph Heuck
> Albert Einstein College of Medicine
> 
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