"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
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
