[R] change fold from package"DEDS"

Hi all: package"DEDS" can find out differentially expressed genes via computing changefold. But if there're 3(or more)groups(1\2\3 for instance),I wanna know the which "group vs group" the changefold is referd to(1 vs 2/1 vs 3/2 vs 3 for instance)? Thanks a lot! My best! _

[R] add info

hi all: If there's a dataframe: x y 1 a 2 b 3 c The info of the data such as : name date author The result I want is: name date author x y 1 a 2 b 3 c In other words,I wanna add the info above the dataframe. How can I do it ? Thanks a lot! My best

[R] a question about "sign" of "cgh" package

Hi all : I'm a user of "cgh" package. Here's a question about "sign". As to help on "sign": sign = +1 is used to detect polysomy (regions of copy number change increase) in test:control logratios. sign = -1 is used ¨C inverting the sign of the logratios ¨C to detect deletions (regions of co

[R] about hcluster

Hi all: As to hcluster,how can I control the cluster is performed according to rows(genes for instance) or columns(samples for instance)? I can't find the parameters for it. Thanks a lot! My best! __ R-help@stat.math.ethz.ch mailing list https://stat.

[R] color key of heatmap.2

Hi all: The color key of heatmap.2 is as follows if I use redgreen style: low level:red high leve:green And what I want is: low level:green hight level:red How can I do it then? Thanks a lot for your help! My best! __ R-help@stat.math.ethz.ch mailing

[R] the legend of heatmap.2

Hi all: As to the legend of heatmap.2,it seems that the legend can only show the distribution of Z score. If I wanna the legend show the distribution of the original data,how can I do it? Thanks a lot for your help. My best! __ R-help@stat.math.ethz.

[R] heatmap

Hello sir; I use the function "heatmap.2" to draw a heatmap of microarray data,which consists of logratios. Q1 But the lengend shows the Z score and the corresponding color.But I want the legend to show the logratios and the corresponding color.How can I do it? Q1 How can I control that cluster

[R] "class" package

Hello sir: Where can I download the package "class"? What I can find is only: http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/class/html/00Index.html But I can't find where I can download it. Thanks! __ R-help@stat.math.ethz.ch mailing list https:

[R] sort dataframe

Hello sir: How can I sort a dataframe by sorting one of its column? e.g. dataframe: id x y a 0.1 3 b 0.5 1 c 0.2 9 d 05 I want the dataframe sorted according to y accending,the result is: id xy b 0.5 1 a 0.1 3 d 05 c 0.2 9 Thanks a lot! My best __

[R] 2 axes in an coordinate system

Hello sir: I wanna get such kind of plot: x : location of chromosome y_left: p value y_right: logratio In other words,On the left side of plot,y is p value;On the right side of plot,y is logratio How can I do it via R command? Thanks a lot! My best! ___

[R] line plot

Hello sir: I wanna get such kind of plot: a line whose start point is(1,10),end point is(5,10) In other words: How can I draw a line if I only know the coordinate of the start point and end point? Thanks! My best __ R-help@stat.math.ethz.ch mailin

[R] plot

Hello sir: a data with 2 columns: id x a 1 b 2 c 3 I wanna get such kind of plot: x: a b c y:1 2 3 But the plot command doesn't permit string character as x. How can I get it ? Thanks a lot ! My best __ R-help@stat.math.ethz.ch mailing list https

[R] digital length

Hell sir: How can I control the digital length of data? e.g: 0.1234 is the output of an algorithm. What I want is 0.12 instead. How can I get this ? Thanks a lot! My best __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/

[R] exact 95% confidence intervals

Hello sir: As to the 2*2 table format for reporting results comparing a new test to true diagnosis,when I got the sensitivity and specificity,how can I calculate the exact 95% confidence intervals (based on the binomial distribution) for sensitivity and specificity via R? Thanks a lot! My bes

[R] about BATCH and parameter file

Hello sir: I use Rcmd to execute R code,such as : "C:\\Program Files\\R\\R-2.2.1\\bin\\Rcmd.exe" BATCH globalLowessRun.r globalLowessRun.r is a R function written by myself. But I wanna make the "globalLowessRun.r" changeable,such as globalLinearRun.r or gridbasedLowessRun.r,and so on. How can

[R] S curve via R

Hello sir: How can I get "S curve" function via R? For SPSS,the function is:y=exp(b0+b1/x) Thanks a lot! -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-i

[R] a question about data combination

Hello sir: Here's the data: a b c d 1 2 3 4 I wanna know how to get: ab ac ad bc bd cd 12 13 14 23 24 34 Thanks a lot! My best -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijin

[R] about string

Hello sir: There are 2 questions about string. 1 How to calculate the width of a string? e.g string "abc"'s width is 3; 2 How can I get the "substring" in such kind of condition: "f:\\JPCS_signal.txt" "f:\\PC1_signal.txt" "f:\\PC2_signal.txt" What I wanna get is "JPCS" "PC1" "PC2".How can I a

[R] seperate strings

x<- "a;b;c;d" How can I get: "a" "b" "c" "d"? Thanks a lot! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

[R] about vsn

Hi all: As to vsn package,how can I transform my raw data format to the demo data of vsn(named "kidney")? My raw data: namesignal dye gene1 815.32 green gene2 671.66 green gene3 713.93 green gene4 703.97 green gene5 493.59 green gene6 477.92 green gene7 346.55 green

[R] about "intersection set" and "union set"

Hello sir: group1:1,2,3,4 group2:1,3,4,5 group3:2,4,8,9 .. ... group1000:9,3,8,2 I wanna get the "intersection set" and "union set". I've tried command "setdiff"and "union",but only two groups is permited.How can I deal with multi groups to find the "intersection set" and "union set"? T

[R] about McNemar

Hello sir: How can I perform McNemar (paired chi square test) by using R? Thanks! -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics & Softwa

[R] u value

As to the standard normal sidtribution,if alpha=0.05(2 tailed),how can I get the "u value" by using R command? p.s result: u value is 1.96. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the postin

[R] u value

As to the standard normal sidtribution,if alpha=0.05(2 tailed),how can I get the "u value" by using R command? p.s result: u value is 1.96. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the postin

[R] read file of EXCEL format

Hello sir: How can I read data file of EXCEL format from disk("d:\\data.XLS" for example)? I can only read data file of .txt format read.delim("d:\\data.txt",header=T,as.is=T),but only EXCEL format is available at present. Thanks a lot __ R-help@st

[R] about list

Hello sir: A question about the usage of list: The data of a list: [[1]] genename comp diff lwr uprp.adj g2-g1 NewU1-R g2-g1 -242.6667 -337.9602 -147.3732 1.754308e-04 g3-g1 NewU1-R g3-g1 -266.6667 -361.9602 -171.3732 8.869357e-05 g4-g1 NewU1-R g4-g1 440.6667