[R] question related to multiple regression

Hi, I am conducting an association analysis of genotype and a phenotype such as cholesterol level as an outcome and the genotype as a regressor using multiple linear regression. There are 3 possibilities for the genotype AA, AG, GG. There are 5 people with the AA genotype, 100 with the AG genoty

Re: [R] power?

an, February 2001, Vol. 55, No. 1, pp 19-24 > > Don't bother with your power analysis, unless you are planning a new > experiment. > > Simon. > > On Tue, 2009-10-06 at 13:49 -0700, SNN wrote: >> Hi, >> >> I have used multiple linear regression on a dat

[R] Power for Multiple regression?

Hi All, I came across this problem which is more a statistical question, I am hoping that some one can clarify this for me Is there a rule of thumb to determine how large your sample size should be before you perform multiple regression. I have search the web and I found some online tools where

[R] power?

Hi, I have used multiple linear regression on a data set and one if the regressor was significant with a p-value =0.01 I need to calculate the power for a multiple linear regression. i.e. do I have enough power to believe the above p-value? -- View this message in context: http://www.nabb

[R] what is the difference between the two logistic models?

Hi All, I have data with 400 individuals and the following information Grade: pass or fail coded as 1 for pass and 0 for fail Sex: male or female ( coded as 1 for male and 2 for female ) Age Teaching.method : can be 1,2,3 I want to fit a logistic regression where the outcome if (1=pass

[R] logistic regression

Hi All, I have data with 400 individuals and the following information Grade: pass or fail Sex: male or female Age Teaching.metho : can be 1,2,3 TotalHours: can be 0,1,2 I want to fit a logistic regression and for the TotalHours I am getting nothing! What could be the reason. What does the

[R] Problem with modifying a data frame

Hi All, this could be a simple question but I am looking into modifying a data frame using a "condition" without the need to loop over that data, would that be possible? I have tried the following > x<-c(4,5,6,6,8) > y<-c("a","b","b","b","c") > data<-data.frame(x,y) > data x y 1 4 a 2 5 b 3

[R] Chi-squared approximation may be incorrect

Hi, I am trying to run a Chi squre test but I am getting the following message Warning messages: 1: In chisq.test(t) : Chi-squared approximation may be incorrect Does anyone what it means? your help is appreciated -- View this message in context: http://www.nabble.com/Chi-squared-approxi

Re: [R] should I use rbind in my example?

'list' and then write your own specialized print > routine. > > On Wed, Jan 21, 2009 at 10:30 AM, SNN wrote: >> >> Hi, >> >> I need to rbind two data frames. Each one has a header . after the rbind >> I >> would like to keep the header for

[R] should I use rbind in my example?

Hi, I need to rbind two data frames. Each one has a header . after the rbind I would like to keep the header for each and have the two data frames separated by a line. Is this possible to do in R? For example weight_meanweight_sd.dev > F 14.3 4.932883 > M 34.7 10.692677 > >

[R] problem with rbind

Hi All, I have a problem with rbind. I have data that consist of weight height .. etc of 1000 patients. I would like to find the mean and the standard deviation ( for the weight , height etc) for each gender. data<-read.table("data.txt", header=T, sep='\t') fdata=NULL for (i in 1:50){ nn<-na

Re: [R] colored 3d scatter plot

Thank you all for your help. SNN wrote: > > > > Hi All, > > I have data for two groups, group with 100 points and group B with 15 > points. i needed plot these two groups in one scatter plot, each group > with a different color. I tried > > plot3d(data, col =

Re: [R] colored 3d scatter plot

I tried scatterplot3d(data, color = rep(c("red", "blue"), c(100, 15)), pch=16) and I am getting the following error message, Error in plot.xy(xy.coords(x, y), type = type, ...) : invalid color name Does anyone know what he problem is? -- View this message in context: http://www.na

[R] colored 3d scatter plot

Hi All, I have data for two groups, group with 100 points and group B with 15 points. i needed plot these two groups in one scatter plot, each group with a different color. I tried plot3d(data, col = c("red", "blue")[c(rep(1, 100), rep(2, 15))], pch=20) . this works but the graph does not look

Re: [R] Plot Principal component analysis

pe="p", highlight.3d=T, pch=16) where the graph looks much nicer but i do not know how to have each group with a different color. Does anyone know how to do it? SNN wrote: > > Hi, > > I have matrix of 300,000*115 (snps*individual). I ran the PCA on the > covariance mat

Re: [R] Plot Principal component analysis

Thanks for your help, Can R plot the data in 3 dimention, with different colors for each group ? for exmple I would like to have the plot with respect to PC1, PC2 and PC3. Thanks, SNN wrote: > > Hi, > > I have matrix of 300,000*115 (snps*individual). I ran the PCA on the

[R] Plot Principal component analysis

Hi, I have matrix of 300,000*115 (snps*individual). I ran the PCA on the covariance matrix which has a dimention oof 115*115. I have the first 100 individuals from group A and the rest of 15 individuals from group B. I need to plot the data in two and 3 dimentions with respect to PC1 and PC2 and

Re: [R] Principal component analysis PCA

> larger data sets where the entire data matrix doesn't fit in memory, you > need some sort of double loop. > > -thomas > > >> Zhaoming >> -Original Message- >> From: SNN [mailto:[EMAIL PROTECTED] >> Sent: Wednesday, February 13, 2008 9

[R] Principal component analysis PCA

Hi, I am trying to run PCA on a set of data with dimension 115*300,000. The columns represnt the snps and the row represent the individuals. so this is what i did. #load the data code<-read.table("code.txt", sep='\t', header=F, nrows=30) # do PCA # pr<-prcomp(code, retx=T, center=T) I a

[R] Principal Components Analysis

Hi, I do have a file that has 50 columns and 40 rows. I want to apply PCA on that data and this is what I did h1<-read.table("Ccode.txt", sep='\t', header=F) # reads the data from the file Ccode.txt h2<-prcomp(na.omit(h1),center=T) but I am getting the following error "Error in svd(x, n