R help - Oct 2011 - FOR loop with statistical analysis for microarray data

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

"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
>
> ______________________________________________
> 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.
David Winsemius, MD
West Hartford, CT

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.
>

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@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@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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