[R] change fold from packageDEDS
Hi all: packageDEDS 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-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 and provide commented, minimal, self-contained, reproducible code.
[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-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 and provide commented, minimal, self-contained, reproducible code.
[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.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] 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 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] 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 only applied to genes(rows) or samples(columns) via heatmap.2 function?Default is cluster applied to both rows and columns. Thanks a lot! My best! __ 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 and provide commented, minimal, self-contained, reproducible code.
[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.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 and provide commented, minimal, self-contained, reproducible code.
[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://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] 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-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 and provide commented, minimal, self-contained, reproducible code.
[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-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 and provide commented, minimal, self-contained, reproducible code.
[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 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] 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://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] 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-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[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 best! -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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 and provide commented, minimal, self-contained, reproducible code.
[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 I achieve this goal via Rcmd.exe BATCH ? The only finding is: Rcmd BATCH [options] globalLowessRun.r [outfile] I wonder the only way I can try is [options],but I don't know how to do it. Thanks a lot! My best -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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 and provide commented, minimal, self-contained, reproducible code.
[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-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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 and provide commented, minimal, self-contained, reproducible code.
[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 Beijing Biochip Technology BioPharma-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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 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 achieve them by R cammand? Thanks a lot! My best -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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] 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-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 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 setdiffand union,but only two groups is permited.How can I deal with multi groups to find the intersection set and union set? Thanks a lot! My best -- *** Xin Meng Capitalbio Corporation National Engineering Research Center for Beijing Biochip Technology BioPharma-informatics Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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 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 Software Dept. Research Engineer Tel: +86-10-80715888/80726868-6438 Fax: +86-10-80726790 [EMAIL PROTECTED] Address:18 Life Science Parkway, Changping District, Beijing 102206, China __ 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] 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 posting guide! http://www.R-project.org/posting-guide.html
[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@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 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 345.3732 535.9602 2.055929e-06 [[2]] genename comp diff lwruprp.adj g2-g1 NewU1-R g2-g1 -242.6667 -337.9602 -147.37315 1.754308e-04 g3-g2 NewU1-R g3-g2 -24. -119.2935 71.29352 8.497181e-01 g4-g2 NewU1-R g4-g2 683. 588.0398 778.62685 4.785440e-08 [[3]] genename comp diff lwruprp.adj g3-g1 NewU2-R g3-g1 -266.6667 -361.9602 -171.37315 8.869357e-05 g3-g2 NewU2-R g3-g2 -24. -119.2935 71.29352 8.497181e-01 g4-g3 NewU2-R g4-g3 707. 612.0398 802.62685 3.713499e-08 [[4]] genename comp diff lwr uprp.adj g4-g1 NewU2-R g4-g1 440.6667 345.3732 535.9602 2.055929e-06 g4-g2 NewU2-R g4-g2 683. 588.0398 778.6268 4.785440e-08 g4-g3 NewU2-R g4-g3 707. 612.0398 802.6268 3.713499e-08 Actually, [[1]] and [[2]] are from the same group, [[3]] and [[4]] are from the same group. And how can I arrange [[1]] [[2]] together(the same as [[3]] and [[4]])? In other words,the result I want is: group1 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 345.3732 535.9602 2.055929e-06 group1 genename comp diff lwruprp.adj g2-g1 NewU1-R g2-g1 -242.6667 -337.9602 -147.37315 1.754308e-04 g3-g2 NewU1-R g3-g2 -24. -119.2935 71.29352 8.497181e-01 g4-g2 NewU1-R g4-g2 683. 588.0398 778.62685 4.785440e-08 group2 genename comp diff lwruprp.adj g3-g1 NewU2-R g3-g1 -266.6667 -361.9602 -171.37315 8.869357e-05 g3-g2 NewU2-R g3-g2 -24. -119.2935 71.29352 8.497181e-01 g4-g3 NewU2-R g4-g3 707. 612.0398 802.62685 3.713499e-08 group2 genename comp diff lwr uprp.adj g4-g1 NewU2-R g4-g1 440.6667 345.3732 535.9602 2.055929e-06 g4-g2 NewU2-R g4-g2 683. 588.0398 778.6268 4.785440e-08 g4-g3 NewU2-R g4-g3 707. 612.0398 802.6268 3.713499e-08 Thanks! My best __ 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
