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Hi, How can I configure R to allow http connection (through company firewall)? Your help are greatly appreciated! Wei Ding, Ph.D. Schering-Plough Research Institute 2015 Galloping Hill Road Kenilworth, NJ 07033 Tel: (908) 740-2592 Fax: (908) 740-7664 ********************************************************************* This message and any attachments are solely for the intended rec... [[dropped]]

...For ( d in 71:75) { Dir<-paste("C:/Awork/geneAssociation/removed8samples/neuhausen", i, sep="") setwd(Dir) .......... then I do not know how to create objects seg71 to seg75; in SAS, it would be seg&d ; I like R, but not good at R. Can you help me? Thank you, Ding --------------------------------------------------------------------- -SECURITY/CONFIDENTIALITY WARNING- This message (and any attachments) are intended solely f...{{dropped:22}}

...having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Mar 5, 2018 at 2:03 PM, David Winsemius <dwinsemius at comcast.net> wrote: > > > On Mar 5, 2018, at 8:52 AM, Ding, Yuan Chun <ycding at coh.org> wrote: > > > > Hi Bert, > > > > I am very sorry to bother you again. > > > > For the following question, as you suggested, I posted it in both > Biostars website and stackexchange website, so far no reply. > > > &g...

...last three dishes to add both A and B drugs. After drug treatments, they measure DNA methylation and genes or gene expression as outcome or response variables(two differnet types of response variables). My boss might want to find out net effect of drug B, but I think we can not exclude the confounding effect of drugA. For example, it is possible that drug B has no effect, only has effect when drug A is present. I asked my collaborator whey she omitted the fourth combination drugA only treatment, she said it was expensive to measure methylation or gene expression, so they performed the experime...

...ackexchange website, so far no reply. I really hope that you can do me a great favor to share your points about how to explain the coefficients for drug A and drug B if run anova model (response variable = drug A + drug B). is it different from running three separate T tests? Thank you so much!! Ding 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 fourth group of no dru...

Hi Sarah, Thank you so much!! I got your good ideas. Ding -----Original Message----- From: Sarah Goslee [mailto:sarah.goslee at 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 from an external source. Do not open attachments or click...

...ugA/no drugB, yes drugA/yes drug B, omitting the fourth group of no drugA/yes drugB. I think we can not investigate interaction between drug A and drug B, can I still run model using R as usual: response variable = drug A + drug B? any suggestion is appreciated. Thank you very much! Yuan Chun Ding --------------------------------------------------------------------- -SECURITY/CONFIDENTIALITY WARNING- This message (and any attachments) are intended solely f...{{dropped:28}}

...y the stats.stackexchange.com statistical site. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Fri, Mar 2, 2018 at 10:34 AM, Ding, Yuan Chun <ycding at coh.org> wrote: > 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 &g...

...tom line of the function definition. Returning an object and graph the object are different process, I am a beginner for 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.4567 at gmail.com] Sent: Monday, January 15, 2018 10:11 AM To: Ding, Yuan Chun <ycding at coh.org> Cc: Richard M. Heiberger <rmh at temple.edu>; r-help at r-project.org Subject: Re: [R] consolidate three function into one That is certainly OK, but you...

...7ce1122ced92b0374cb0943c252cefce796d9734901bee22dd084c41f1ed488f libref_array-devel-0.1.4-11.el6_8.1.i686.rpm a5a185848a6551acdca74f4ad97e2f34f33a539b5c2e310519f6fea5d52ad6b1 libref_array-devel-0.1.4-11.el6_8.1.x86_64.rpm Source: d256d1ce71b8300c87a579fb78fa30db184ff891a66090defce4f657a81c3e7b ding-libs-0.4.0-11.el6_8.1.src.rpm -- Johnny Hughes CentOS Project { http://www.centos.org/ } irc: hughesjr, #centos at irc.freenode.net Twitter: @JohnnyCentOS

...libpath_utils-0.2.1-10.el5.i386.rpm 00862b65df07ef5f1784d7de25096b35 libpath_utils-devel-0.2.1-10.el5.i386.rpm 373264e916aefeb62a5beaddb053ec51 libref_array-0.1.1-10.el5.i386.rpm a28090c2f428ff1457d91a5bf3964fc0 libref_array-devel-0.1.1-10.el5.i386.rpm Source: df420ace1be9806d9dadc7cf7f299f53 ding-libs-0.1.2-10.el5.src.rpm -- Karanbir Singh CentOS Project { http://www.centos.org/ } irc: z00dax, #centos at irc.freenode.net

...ibref_array-0.1.1-10.el5.i386.rpm 610dbf5a7ae8fdd9d77b0694d0a94a80 libref_array-0.1.1-10.el5.x86_64.rpm 930a70f146580c6de6da15c2035f2bcc libref_array-devel-0.1.1-10.el5.i386.rpm aaa19f094427d63ecb2c33f97ad6df54 libref_array-devel-0.1.1-10.el5.x86_64.rpm Source: df420ace1be9806d9dadc7cf7f299f53 ding-libs-0.1.2-10.el5.src.rpm -- Karanbir Singh CentOS Project { http://www.centos.org/ } irc: z00dax, #centos at irc.freenode.net

Hi Rui, You are always very helpful!! Thank you, I just modified your R codes to remove a row with zero values in both column pair as below for my real data. Ding dat<-gene22mut.coded r <- P <- matrix(NA, nrow = 22L, ncol = 22L, dimnames = list(names(dat), names(dat))) for(i in 1:22) { #i=1 x <- dat[[i]] for(j in (1:22)) { #j=2 if(i == j) { # there's nothing to test, assign correlation 1 r[i, j] &l...

> On Mar 5, 2018, at 8:52 AM, Ding, Yuan Chun <ycding at coh.org> wrote: > > Hi Bert, > > I am very sorry to bother you again. > > For the following question, as you suggested, I posted it in both Biostars website and stackexchange website, so far no reply. > > I really hope that you can do me a gre...

Hi Richard, Thank you so much!! I understand the problem now, I assign a name to the "ggsurvplot" object and then add print(fig) at bottom of function definition, now figure gets printed on screen. Ding # function to generate RFS curves RFS <- function( inputfile, N ) { cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters, data = inputfile) if( N==2) {palette <- c("red", "black") legend.labs <- c("Cluster1", &qu...

...along > and sticking things into it." > > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > > On Mon, Mar 5, 2018 at 2:03 PM, David Winsemius <dwinsemius at comcast.net> > wrote: > > > > > On Mar 5, 2018, at 8:52 AM, Ding, Yuan Chun <ycding at coh.org> wrote: > > > > > > Hi Bert, > > > > > > I am very sorry to bother you again. > > > > > > For the following question, as you suggested, I posted it in both > Biostars website and stackexchange website, so f...

...cat 4 As a single line command: dat1$C <- seq(length(unique(dat1$B)))[ match( dat1$B, unique(dat1$B) )] -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 Lab cell 925-724-7509 ?On 5/11/18, 12:04 PM, "R-help on behalf of Ding, Yuan Chun" <r-help-bounces at r-project.org on behalf of ycding at coh.org> wrote: Hi Sarah, Thank you so much!! I got your good ideas. Ding -----Original Message----- From: Sarah Goslee [mailto:sarah.goslee at gmail.com] Sent: Friday, May 11, 20...

Hi Rui, Thank you very much! Yes, I verified using real data, it worked correctly as expected after adding tidyr:: to the pivot_longer function and dplyr:: to the group_by and summarize Function. I did not know how to assign the tidyr and dplyr to the three functions because I do not really understand well the three functions and just got the code from a google search. I also tried your simplified cod...

...function returns, which you might find useful. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Jan 15, 2018 at 9:57 AM, Ding, Yuan Chun <ycding at coh.org> wrote: > Hi Richard, > > Thank you so much!! I understand the problem now, I assign a name to the > "ggsurvplot" object and then add print(fig) at bottom of function > definition, now figure gets printed on screen. > > Ding >...

> On Mar 5, 2018, at 3:04 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > > But of course the whole point of additivity is to decompose the combined effect as the sum of individual effects. Agreed. Furthermore your encoding of the treatment assignments has the advantage that the default treatment contrast for A+B will have a statistical estimate associated with it. That was a deficiency of my encoding that Ding found problematic. I did have the incorrect notion that the encoding of Drug B in the single drug situation...