[R] FOR loop with statistical analysis for microarray data

[Weidong Gu]

In your loop, you assign, for example, pv twice
pv=w$p.value # pv is scalar
pv[i]= w[2]   # pv is a vector

give an example for the point

pv=1
pv[5]=2
pv
[1]  1 NA NA NA  2

This may not be what you want.

Weidong

On Thu, Oct 27, 2011 at 7:40 AM, Seb <seba.bat at gmail.com> wrote:
> 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 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
>> >
>> > ______________________________________________
>> > R-help at 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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>
> ______________________________________________
> R-help at 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.
>