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

[Christoph Heuck]

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]))

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