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....@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
>
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>
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