Re: [R] how to estimate treatment-interaction contrasts

Hello, R experts, Could I use the command suggested by Chunk to get the estimates for treat-interaction contrasts (non-orthognal) which indicates below: summary(lm(score ~ A*B)) or is there any other ways to get the estimates? Again, Chunk, thank you for your help! Joshua Quoting Chuck Cleland

Re: [R] how to estimate treatment-interaction contrasts

Hello, Chuck, Thank you very much for your help! But the contrasts I want to do simutaneously is contrasts(B) [,1] [,2] [,3] [,4] b1 -4 -3 -2 -1 b21 -3 -2 -1 b312 -2 -1 b4123 -1 b51234 Could you please show me how to calculate

[R] how to estimate treatment-interaction contrasts

Hello, R experts, Sorry for asking this question again again since I really want a help! I have a two-factor experiment data and like to calculate estimates of interation contrasts say factor A has levels of a1, a2, and B has levels of b1, b2, b3, b4, and b5 with 3 replicates. I am not sure the

[R] how to calculate interaction contrast

Hello, R experts, Sorry for asking this question again since I really want a help! I have a two-factor experiment data and like to calculate estimates of interation contrasts say factor A has levels of a1, a2, and B has levels of b1, b2, b3, b4, and b5 with 3 replicates. I am not sure the

[R] interaction contrast

Hello, R experts, Sorry for asking this question again since I really want a help! I have a two-factor experiment data and like to calculate estimates of interation contrasts say factor A has levels of a1, a2, and B has levels of b1, b2, b3, b4, and b5 with 3 replicates. I am not sure the

[R] how to calculate estimate of interation contrast in two-factor experiment

Hello, R experts, I have a two-factor experiment data and like to calculate estimates of interation contrasts say factor A has levels of a1, a2, and B has levels of b1, b2, b3, b4, and b5 with 3 replicates. I am not sure the constrast estimate I got is right using the script below:

[R] How to transform matrices to ANOVA input datasets?

Hello, R experts, I have a list called dataHP which has 30 elements (m1, m2, ..., m30). Each element is a 7x6 matrix holding yield data from two factors experimental design, with treatment in column, position in row. For instance, the element 20 is: dataHP[[20]] col1 col2

Re: [R] how to contrast with factorial experiment

Hello, R experts, If I understand Ted's anwser correctly, then I can not contrast the mean yields between sections 1-8 and 9-11 under Trt but I can contrast mean yields for sections 1-3 and 6-11 because there exists significant interaction between two factors (Trt:section4, Trt:section5).

Re: [R] how to contrast with factorial experiment

Hello, Ted, Thank you for your help! So I can not contrast the mean yields between sections 1-8 and 9-11 under Trt but I can contrast mean yields for sections 1-3 and 6-11 because there exists significant interaction between two factors (Trt:section4, Trt:section5). Could I use the commands

[R] how to constrast with factorial experiment

Hello, R users, I have two factors (treat, section) anova design experiment where there are 3 replicates. The objective of the experiment is to test if there is significant difference of yield between top (section 9 to 11) and bottom (section 9 to 11) of the fruit tree under treatment. I

Re: [R] operations on a list

Hello, Jacques, Thank you very much for your help! It's clever code and works fine. But I don't understand what the last line code is for. Should I really need the last line? Thanks again. Josh Quoting Jacques VESLOT [EMAIL PROTECTED]: you could try : trt1 - do.call(rbind, lapply(listexp,

[R] operation on a list

Hello, R Users, I have a list (say listexp) of 10,000 elements, each of which consists of a matrix (5X6). It likes: $a trt1rep1trt1rep2trt2rep1trt2rep2ctlrep1ctlrep2 [1,] 5054 98 8940 45 [2,] 6065 76 79

Re: [R] Operations on a list

Hello, Everyone, I am sorry that my message got truncated. I resend it again as below: Hello, R Users, I have a list (say listexp) of 10,000 elements, each of which consists of a matrix (5X6). It likes: $a trt1rep1trt1rep2trt2rep1trt2rep2ctlrep1ctlrep2 [1,] 5054

Re: [R] operations on a list

Hello, Everyone, I am sorry that my message got truncated due to wrong format. I hope it works now: Hello, R Users, I have a list (say listexp) of 10,000 elements, each of which consists of a matrix (5X6). It likes: $a trt1rep1trt1rep2trt2rep1trt2rep2ctlrep1ctlrep2 [1,]

[R] how to make a sub list from a long list using the component name?

Hello, R users, I have a long list with over 20,000 elements (say foo), now I want to make a sub list of 30 elements from this list using the component names such as subname-c( a, b, d, f, g, h, o, q,...). One way to do it is to make rest of elements in the list NULL, that is too silly. Is there

Re: [R] Why I can't retrieve GO identifier correctly?

Hello, Uwe and Robert, Thank you for your help! I fixed the problem as your suggestion. I run into a new issue: I can't sink the output to a file in the script within loops as bellows, but I can sink it in the command line( I run R1.9.1 on WinXP). The scrip: sink(C:/level3BPterm.txt)

[R] Why I can't retrieve GO identifier correctly?

Hello, R experts, I tried to retrieve all biological process GO terms at level 3 starting biological process as level 1 using the code as bellows: 1 library(GO) 2 library(GOstats) 3 level2-getGOChildren(GO:0008150)$GO:0008150$Children 4 for ( i in 1:length(level2)) { 5level3 -

[R] how to in XML on windows XP for R 1.9.1

Dear R experts: I tried two ways to install Package:XML on windows xp for R 1.9.1, all failed. Messages are given as bellows: 1 download from CRAN install.packages(XML, CRAN = getOption(CRAN), + contriburl = contrib.url(http://cran.r-project.org;), + available = NULL, destdir = NULL, +

[R] how calculate mean for each group

Hello, R experts: I got data like this: group duplicate treatment A Y 5 A Y 3 A N 6 B Y 2 B N 4 B Y 1 How to sort the data and calculate the average treatment value for each group in two

[R] what does this error mean?

Dear R-users: I am runing R 1.6.2 with Windows XP. I try to calculate Pearson correlation and Spearman correlation of any pairwise columns of 8000 x 80 data matrix with missing values and randomize the matix 1000 times and calculate this two correlations again. The code bellow for Pearson is

[R] how to calculate Spearman correlation with missing values

Hello, there: I got data matix with missing values. I want to calculate any possible pairwise Spearman correlation rho for each column. Is there a function just like cor(x, y, use=complete.obs) for Pearson correlation? Thanks in advance! Josh __

[R] how to randomize data matrix

Dear R users: Is there a function or easier way to randomize the data between rows (considering a row as a whole unit)? For example, original data: A1 A2 A3 A4 B1 1 2 3 4 B2 5 6 7 8 B3 9 10 11 12 B4 13 14 15 16 randomized data: A1 A2 A3 A4 B4 13 14 15 16 B2 5 6

[R] Zero is not zero

Hello, There: I read data from tab-delimted text file(1888.txt) in C:/temp, which has thousands rows and 80 colulms, using read.delim(C:/temp/1888.txt). when I retrieved the numeric coulum which has real zero values and applies R buid-in function such as mean( ), sum() and got a result of NA.