Looks like you have problems with indexing. In your code, fc is a
vector of length 2, pv is a scalar(it only keeps the last value of the
loop), then you try to cbind different lengths of vectors
(row.names(y1), fc and pv). cbind only works for vectors with the same
length.
I don't know what you want to achieve, but you can keep p.value using
pv[i]. In the previous code, you reassiged pv before pv[i]. So your
1st assignment of pv wiped out pv vector. You need to read helps about
indexing, vectors.
Weidong
On Thu, Oct 27, 2011 at 10:41 AM, Seb <seba....@gmail.com> wrote:
> 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.
>>>
>>
>
______________________________________________
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.
