thanks for the replies.... so, i remove the indices pv[i] and
fc[i]..but when i run it like this:
===============
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$p.value
}
results = cbind(row.names(y1), fc, pv)
head(results)
=================
i get
===========
Warning message:
In cbind(row.names(y1), fc, pv) :
number of rows of result is not a multiple of vector length (arg 2)
=============
and the "fc" values are repeated over until the end of the rows and
the "pv" is the same all across the samples...how can i fix it?!
...i apologize if it's a silly situation but i'm new to this and can't
get my head around it!
thanks so much!!
On Thu, Oct 27, 2011 at 9:02 AM, Weidong Gu <anopheles...@gmail.com> wrote:
> In your loop, you assign, for example, pv twice
> pv=w$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....@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....@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.
>>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> 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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