y1,y2 were designed as follow,from the original data file :
y1=data[,1:2]
y2=data[,3:4]

...I am a bit confused with what "redesign the whole vector again" and
"specify indices twice " actually mean?...could u point it out in the
script?

Thanks so much I really appreciate it!!

Sent from my -DROID-

On Oct 26, 2011 6:56 PM, "Weidong Gu"  wrote:
>
> If you provide an example data (y1 and y2 in the loop), you might have
> got specific helps already. A few things in your loop seem suspicious.
> fc and pv are vectors, and in each loop you redesigned the whole
> vectors and specific indices twice. That may cause your problems.
>
> Weidong Gu
>
>
>
> On Wed, Oct 26, 2011 at 4:56 PM, Seb <seba.bat@gmail.com> wrote:
> > hi all
> >
> > i started recently using R and i found myself stuck when i try to
> > analyze microarray data.
> >
> > i use the "affy" package to obtain  the intensities of the probes, i
> > have two CTRs and two treated.
> >
> >  HG.U133A.Experiment1.CEL HG.U133A.Experiment2.CEL
> > HG.U133A_Control1.CEL HG.U133A_Control2.CEL
> > 1007_s_at               2156.23115                467.75615
> >  364.60615             362.11865
> > 1053_at                   88.76368                 93.58436
> >  438.49365             357.75615
> > 117_at                   144.00743                101.26120
> >  95.11117             107.01623
> > 121_at                   551.36865                639.45615
> >  456.66865             435.95615
> > 1255_g_at                 65.33164                 18.39570
> >  14.22565              20.74632
> > 1294_at                  106.19083                169.69369
> >  78.15722              81.14689
> >
> > i divided the first two columns in two data.frames to divide Experim and
CTRs
> >
> > then, i created a FOR loop to create a vector per each row containing
> > a vector with two values per each gene and i wanted to do a
> > Wilcox.test to obtain the significant genes..BUT i get a list of NULL
> > like you can see here
> > ..the first row works but then i get NULL down till the end of the
array...
> >
> >                fc        pv
> > [1,] "1007_s_at" -20.248   0.4664612
> > [2,] "1053_at"   -344.7132 NULL
> > [3,] "117_at"    NULL      NULL
> > [4,] "121_at"    NULL      NULL
> > [5,] "1255_g_at" NULL      NULL
> > [6,] "1294_at"   NULL      NULL
> >
> > the script i used is:
> > ===================
> > fc=0
> > pv=0
> > for (i in 1:nrow(data))
> > {
> >        v1= c(y1[i,1], y1[i,2])
> >        v2= c(y2[i,1], y2[1,2])
> >        fc=v1-v2
> >        w=t.test(v1,v2)
> >        pv=w$p.value
> >        fc[i]= w[1]
> >        pv[i]= w[2]
> > }
> >
> > results = cbind(row.names(y1), fc, pv)
> >
> > head(results)
> >
> > ================
> >
> > what did i do wrong? i can't find a way around this!!!
> >
> > thanks so much!!!
> >
> > Seb
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >

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