HI All,
Sorry to bother you.
I have a data matrix with 1000 genes in rows and 100 samples in columns; I
need to run Cox regression model for each of the 1000 markers. I know how to
run Cox regression model for individual marker. Does anyone know a R package or
method to run Cox model for tho
HI R users,
I construct dendrogram tree and cut the tree into different clusters, then
generate survival curves by the following three functions. All variables are
included in an inputfile.
Can you help me to consolidate the following three function into one functions?
I thought about using
.
Thanks,
Ding
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Sunday, January 14, 2018 9:50 AM
To: Ding, Yuan Chun
Subject: Re: [R] consolidate three function into one
I have not looked at your code *at all*, so I am not sure what exactly you mean
by "consolidate."
Is this wh
main = "Survival curve",pval = TRUE,font.x = 16,font.y = 16,
font.tickslab = 14,font.legend =c(14,"plain","black"),
legend = "bottom",
legend.title = "Tree Cluster",
legend.labs = legend.labs,
s)",
main = "Survival curve",pval = TRUE,font.x = 16,font.y = 16,
font.tickslab = 14,font.legend =c(14,"plain","black"),
legend = "bottom",
legend.title = "Tree Cluster",
legend.labs = legend.labs
writing R
function and need to find a good guide source about writing R functions. If
you know a good book or website for guidance of R function, please let me know.
Thanks,
Ding
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Monday, January 15, 2018 10:11 AM
To: Ding, Yuan Chun
Cc
Hi R Users,
I am very frustrated with the following code. Please do me a favor to run it.
after reading into the test data set (I also pasted the data set below), the
first line of code for "res_coxphf" did not work and generated the error code
below. but the other three line worked well. the
Dear R users,
I need to analyze data generated from a partial two-by-two factorial design:
two levels for drug A (yes, no), two levels for drug B (yes, no); however,
data points are available only for three groups, no drugA/no drugB, yes
drugA/no drugB, yes drugA/yes drug B, omitting the fourt
Hi Bert,
Thank you so much for your direction, I have asked a question on stackexchange
website.
Ding
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Friday, March 02, 2018 12:32 PM
To: Ding, Yuan Chun
Cc: r-help@r-project.org
Subject: Re: [R] data analysis for partial two-by-two
= drug A + drug B?
any suggestion is appreciated.
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Friday, March 02, 2018 12:32 PM
To: Ding, Yuan Chun
Cc: r-help@r-project.org
Subject: Re: [R] data analysis for partial two-by-two factorial design
[Attention
, March 05, 2018 2:27 PM
To: David Winsemius
Cc: Ding, Yuan Chun; r-help@r-project.org
Subject: Re: [R] data analysis for partial two-by-two factorial design
David:
I believe your response on SO is incorrect. This is a standard OFAT (one factor
at a time) design, so that assuming additivity (no
-help-boun...@r-project.org] On Behalf Of Ding, Yuan Chun
Sent: Monday, March 05, 2018 2:45 PM
To: Bert Gunter; David Winsemius
Cc: r-help@r-project.org
Subject: Re: [R] data analysis for partial two-by-two factorial design
Hi Bert and David,
Thank you so much for willingness to spend some time on
insem...@comcast.net]
Sent: Monday, March 05, 2018 3:55 PM
To: Bert Gunter
Cc: Ding, Yuan Chun; r-help@r-project.org
Subject: Re: [R] data analysis for partial two-by-two factorial design
> On Mar 5, 2018, at 3:04 PM, Bert Gunter wrote:
>
> But of course the whole point of additivity is to
Dear R users,
I got the following error message from running sqldf code in R. do you know
how to fix it? I read the sqldf package instruction and did not find a
solution.
Thank you,
Ding
chr10 <- sqldf("select * from manifest where CHR==10")
UCN3cpg <- sqldf("select * from chr10 where MA
Hi All..,
I need to do the following repetitive jobs:
seg71 <-
read.csv("C:/Awork/geneAssociation/removed8samples/neuhausen71/seg.pr3.csv",
head=T)
seg71$id <-"sn71"
seg72 <-
read.csv("C:/Awork/geneAssociation/removed8samples/neuhausen72/seg.pr3.csv",
head=T)
seg72$id <-"sn72"
seg73 <-
rea
Hi Rui,
Thank you very much!! It worked very well, I am looking into how to use
lapply and do.call.
Ding
-Original Message-
From: Rui Barradas [mailto:ruipbarra...@sapo.pt]
Sent: Monday, April 16, 2018 2:16 PM
To: Ding, Yuan Chun; r-help@r-project.org
Subject: Re: [R] how to write a
No, I do not use gmail, still got dirty spam email twice.
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Fowler, Mark
Sent: Tuesday, April 17, 2018 12:32 PM
To: Luis Puerto; Peter Langfelder
Cc: R-Help ML R-Project; Neotropical bat risk assessments
Subj
Dear R users,
I need to merge two data frames based on both equal and unequal comparisons.
The "sqldf" package used to work well , but today, I cannot resolve the
following error by reinstallation of the sqldf package. Can anyone suggest a
different way to perform this kind of merge function
;- sqldf("select * from DMR_log2pbde47 as a left join
DMS_log2pbde47 as b
on a.chrom = b.chromo and a.start <= b.MAPINFO and
a.end >= b.MAPINFO", method = "raw" )
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org]
Hi All,
I want to create a categorical variable, cat.pfoa, in the file of pfas.pheno (a
data frame) based on log2pfoa values. I can do it using the following code.
pfas.pheno <-within(pfas.pheno, {cat.pfoa<-NA
cat.pfoa[pfas.pheno$log2pfoa <=quantile(pfas.pheno$log2pfoa,0.25, na.rm
=T)]<-0
c
Hi Rui,
Thank you very much for your help!! It works very well, I got it.
Ding
-Original Message-
From: Rui Barradas [mailto:ruipbarra...@sapo.pt]
Sent: Thursday, April 19, 2018 11:35 AM
To: Ding, Yuan Chun ; r-help@r-project.org
Subject: Re: [R] create multiple categorical
Hi David,
Thank you so much for your kind suggestion and fixing my code!! I learn a lot
from you today.
Ding
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, April 19, 2018 6:58 PM
To: Ding, Yuan Chun
Cc: r-help@r-project.org
Subject: Re: [R
Hi All,
I have a data frame dat1:
dat1 <-data.frame(N=seq(1, 12,1), B=c("29_log","29_log", "29_log", "27_cat",
"27_cat",
"1_log",
"1_log", "1_log", "1_log", "1_log",
Hi Sarah,
Thank you so much!! I got your good ideas.
Ding
-Original Message-
From: Sarah Goslee [mailto:sarah.gos...@gmail.com]
Sent: Friday, May 11, 2018 11:40 AM
To: Ding, Yuan Chun
Cc: r-help mailing list
Subject: Re: [R] add one variable to a data frame
[Attention: This email came
h of each value, and unique values
dat1$sarah2 <- rep(seq_len(length(unique(dat1$B))),
times=rle(as.vector(dat1$B))$lengths)
#seq_along(x) is the same as seq_len(length(x))
dat1$D <- rep(seq_along(unique(dat1$B)),
times=rle(as.vector(dat1$B))$lengths)
and then
got answer after coming back from lunch. I am a beginner in R, so question
might be trivial.
Ding
From: Bert Gunter [mailto:bgunter.4...@gmail.com]
Sent: Friday, May 11, 2018 1:37 PM
To: Sarah Goslee
Cc: Ding, Yuan Chun; r-help mailing list
Subject: Re: [R] add one variable to a data
Dear R community,
For 100 sites at human chromosomes, I ran two tests, one is to consider an
experiment measurement as a continuous variable, so doing multiple regression;
the other is to compare top 25% samples to bottom 25% samples based on values
of the measured variable, so categorical an
Hi All,
I generated the attached heatmap using the following R code and attached
testfile.
I tried to move the legend to the bottom, Can anyone help me? I have play for
3 hours and can not resolve the problem.
Thank you,
Ding
--
Hi All,
I generated the attached heatmap using the following R code and attached
testfile.
I tried to move the legend to the bottom, Can anyone help me? I have played
for 3 hours and can not resolve the problem.
I realized that in the last email, I forgot to include the "Group" variable for
Hi David,
Thank you so much!! Problem resolved. xpd=TRUE does the trick to put a legend
outside.
Ding
-Original Message-
From: David L Carlson [mailto:dcarl...@tamu.edu]
Sent: Thursday, October 04, 2018 12:09 PM
To: Ding, Yuan Chun; r-help@r-project.org
Subject: RE: heatmap.2, adding
I want to calculate Euclidean distance between 12 populations, in each
population there are 20 samples and each sample is measured for 100 genes
(these are microarray data; the numbers here are just examples).
The equation I found is:
distance = sqrt{[sum(Average of xi -average of yi)^2] /n },
R package to do it.
Thanks,
Ding
-Original Message-
From: Sarah Goslee [mailto:sarah.gos...@gmail.com]
Sent: Thursday, September 04, 2014 4:49 PM
To: Ding, Yuan Chun
Cc: r-help@R-project.org
Subject: Re: [R] calculate Euclidean distances between populations in R with
this data structure
32 matches
Mail list logo
