[R] cannot open gplots libray
hi all i'm trying to open gplots library but i keep on getting this error: /Loading required package: gdata Error in readRDS(mapfile) : embedded nul in string: 'ref\0\0\002\0\0\0\0' Error : unable to load R code in package ‘gdata’ Error: package ‘gdata’ could not be loaded/ if i run session info the results are: /> print(sessionInfo()) R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] gtools_2.7.0 loaded via a namespace (and not attached): [1] tools_2.15.1 / any idea how to fix this? i updated the packages but it didn't help i run R on Windows 7! thanks! -- View this message in context: http://r.789695.n4.nabble.com/cannot-open-gplots-libray-tp4646352.html Sent from the R help mailing list archive at Nabble.com. __ 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] GSEA package error
Dear R gurus I’m trying to use the GSCA package to a series of microarray data (prostate cancer normal vs tumor (29 vs 29 paired)) but I’m running into some problems. I have a matrix (named /data_final/) with 11k rows(genes) and 60 cols (58 samples (29N vs 29T), GO IDs, KEGG IDs). I also have a separate vector GS with the GO IDs mapped to genes (no duplicate genes but multiple IDs per gene like in col 59) However when I try to run: /singleDC(data_final, group=c(1:29,30,58), GSdefList = GS, nperm = 3, permDI=TRUE)/ I get an error/ “unused argument(s) (permDI=TRUE)”/ When I run it without that argument it runs indefinitely even if I use only 100 rows data_final[1:100,]. Furthermore when I block the computation I get the error: /Error in `[.data.frame`(fixed.gs.data, , (csum.group[i-1] + 1):csum.group[i]) : Undefined colums selected/ If you could give me some ideas on how to have it working that would be extremely useful! Seb -- View this message in context: http://r.789695.n4.nabble.com/GSEA-package-error-tp4651223.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] GSCA package error
it's the GSCA packagei made a typo in the subject, my apologies the package is available from here http://www.biostat.wisc.edu/~kendzior/GSCA/ i am now trying to do co-expression analysis using EBcoexpress but looks like i have a similar problem due to the sample size! thanks! -- View this message in context: http://r.789695.n4.nabble.com/GSEA-package-error-tp4651223p4651310.html Sent from the R help mailing list archive at Nabble.com. __ 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] 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 2156.23115467.75615
364.60615 362.11865
1053_at 88.76368 93.58436
438.49365 357.75615
117_at 144.00743101.26120
95.7 107.01623
121_at 551.36865639.45615
456.66865 435.95615
1255_g_at 65.33164 18.39570
14.22565 20.74632
1294_at 106.19083169.69369
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...
fcpv
[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
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] FOR loop with statistical analysis for microarray data
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 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 2156.23115467.75615
> > 364.60615 362.11865
> > 1053_at 88.76368 93.58436
> > 438.49365 357.75615
> > 117_at 144.00743101.26120
> > 95.7 107.01623
> > 121_at 551.36865639.45615
> > 456.66865 435.95615
> > 1255_g_at 65.33164 18.39570
> > 14.22565 20.74632
> > 1294_at 106.19083169.69369
> > 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...
> >
> >fcpv
> > [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.
Re: [R] FOR loop with statistical analysis for microarray data
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$p.value
}
results = cbind(row.names(y1), fc, pv)
head(results)
=
i get
===
Warning message:
In cbind(row.names(y1), fc, pv) :
number of rows of result is not a multiple of vector length (arg 2)
=
and the "fc" values are repeated over until the end of the rows and
the "pv" is the same all across the samples...how can i fix it?!
...i apologize if it's a silly situation but i'm new to this and can't
get my head around it!
thanks so much!!
On Thu, Oct 27, 2011 at 9:02 AM, Weidong Gu wrote:
> In your loop, you assign, for example, pv twice
> pv=w$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 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 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
>>> > 95.7 107.01623
>>> > 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)
>>> >
>>> >
Re: [R] creating vector os zeros for simulations (beginner's question)
you could try this:
u2=matrix(rnorm(150), nrow=5, ncol=30); u2
Seb
On Thu, Oct 27, 2011 at 1:44 PM, Iara Faria wrote:
> Dear R helpers,
>
> I know this is a simple task, but I'm new to R and I'm still havind
> difficulties with the language.
> I want to create 30 vectors to be used in a simulation, each with 1 columm
> and 5 lines, of random numbers N(0,1).
> What I tried was this:
>
> N=150
> u2<-rep(1:150,0)
> u2<-list(matrix(0,5))
> u2
> for(i in 1:N)
> {
> u2[i]<-rnorm(5)
> }
> u2
>
> ### also tried this:
>
> N=150
> u2<-rep((matrix(0,5)),30)
> u2
> for(i in 1:N)
> {
> u2[i]<-rnorm(5)
> }
> u2
>
>
> The problem is none of this gives me the random numbers arranged in vectors.
> I've tried other variations too, but haven't managed to get it through.
>
> Any help is very welcome.
> Kind regards,
> Iara
> [[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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
