[R] FOR loop with statistical analysis for microarray data

[David Winsemius]

"affy" is a bioconductor package. You should be asking this question  
on the bioc mailing list.

-- 
David.
On Oct 26, 2011, at 4:56 PM, Seb 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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David Winsemius, MD
West Hartford, CT