[R] FOR loop with statistical analysis for microarray data

[Weidong Gu]

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 at 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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