Message-ID: <CAEhWdG5UvCX9a03q_=PaSwfu+havg9Bb9k6vmTRQ46CQk7p7fg@mail.gmail.com>
Date: 2011-10-27T13:02:24Z
From: Weidong Gu
Subject: FOR loop with statistical analysis for microarray data
In-Reply-To: <CANStiKmDkpgWCvQdG3b4R84CBB7vVFFvjSO=FS-uA9WKFucsHA@mail.gmail.com>
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.
>> >
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>