Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (2 genes
x 550 samples) with survival endpoint. It quickly give the following error:
> library(samr)Loading required package: imputeLoading required package:
> matrixStats
Attaching package: ‘matrixStats’
The following objects
Sorry forgot to use plain text format, hope this time it works:
Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (2 genes
x 550 samples) with survival endpoint. It quickly give the following error:
> library(samr)
Loading required package: impute
Loading required package: m
Hi all,
The survdiff() from survival package has an argument "rho" that implements
Fleming-Harrington weighted long rank test.
But according to several sources including "survminer" package
(https://cran.r-project.org/web/packages/survminer/vignettes/Specifiying_weights_in_log-rank_comparison
Thank you David!
On Wednesday, February 14, 2018, 6:05:46 PM PST, David Winsemius
wrote:
> On Feb 14, 2018, at 5:26 PM, David Winsemius wrote:
>
>>
>> On Feb 13, 2018, at 4:02 PM, array chip via R-help
>> wrote:
>>
>> Hi all,
>>
>
Thank you Terry. Right now I can use comp() from survMisc package to do the
2-parameter version of F-H weighting. I think both SAS and stata offer the
2-parameter version, so just thought it would be nice if survdiff() can have
that option given it's standard package in R.
Thanks!
John
On
Dear all, I am new to lattice, so would appreciate anyone's help on the
questions below. I am using xyplot to plot some trend in my dataset. Using the
example dataset attached, I am trying to plot variable "y" over variable "time"
for each subject "id":
dat<-read.table("dat.txt",sep='\t',header=
ouble 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 Sun, Apr 30, 2017 at 6:07 PM, array chip via R-help
> wrote:
>> Dear all, I am new to lattice
Hi, I am running a logistic regression on a simple dataset (attached) using glm:
> dat<-read.table("dat.txt",sep='\t',header=T)
If I use summary() on a logistic model:
> summary(glm(y~x1*x2,dat,family='binomial'))
Coefficients: Estimate Std. Error z value Pr(>|z|)(Intercept)
19.57
Hi,
I am learning to use your gsDesign package! I have a question about Pocock and
OBF boundary. As far as Iunderstand, these 2 boundaries require equal spacing
between interim analyses(maybe this is not correct?). But I can still use
gsDesign to run an analysisbased on unequal spacing:
gsDes
oundary
> On 23 Sep 2017, at 01:32, array chip via R-help wrote:
>
> Hi,
>
> I am learning to use your gsDesign package! I have a question about Pocock
> and OBF boundary. As far as Iunderstand, these 2 boundaries require equal
> spacing between interim analyses(maybe
] https://cran.r-project.org/web/packages/reprex/index.html (read the
vignette)
--
Sent from my phone. Please excuse my brevity.
On September 23, 2017 9:53:05 PM PDT, array chip via R-help
wrote:
>Sorry for messed up text. Here it goes again:
>I am learning to use the gsDesign package.
&
Hello,
Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2 survfit
objects, just like this one:
https://drive.google.com/file/d/1fEcpdIdE2xYtA6LBQN9ck3JkL6-goabX/view?usp=sharing
Suppose I have 2 survfit objects: fit1 is for the curve on the left (survtime
has been truncate
new clipping rectangle will persist until you or
something else resets it.
Jim
On Tue, Sep 29, 2020 at 10:34 AM array chip via R-help
wrote:
>
> Hello,
>
> Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2
> survfit objects, just like this one:
>
&g
0, 1, 0.2), labels = FALSE, lty = "dashed")
Regards,
Marc Schwartz
> On Sep 28, 2020, at 8:33 PM, array chip via R-help
> wrote:
>
> Hello,
>
> Can anyone suggest a simple way to generate a Kaplan-Meier plot with 2
> survfit objects, just like this one:
>
&
direct way would be:
plot(fit1, col=1:2)
xylim<-par("usr")
clip(4,xylim[2],xylim[3],xylim[4])
lines(fit2,col=1:2)
Remember that the new clipping rectangle will persist until you or
something else resets it.
Jim
On Tue, Sep 29, 2020 at 10:34 AM array chip via R-help
wrote:
>
&g
hn,
> Perhaps the most direct way would be:
>
> plot(fit1, col=1:2)
> xylim<-par("usr")
> clip(4,xylim[2],xylim[3],xylim[4])
> lines(fit2,col=1:2)
>
> Remember that the new clipping rectangle will persist until you or
> something else resets it.
>
> Jim
way would be:
>
> plot(fit1, col=1:2)
> xylim<-par("usr")
> clip(4,xylim[2],xylim[3],xylim[4])
> lines(fit2,col=1:2)
>
> Remember that the new clipping rectangle will persist until you or
> something else resets it.
>
> Jim
>
> On Tue, Sep 29, 202
ee that the extra horizontal line on the top.
> >
> > Can you or anyone have any suggestion what went wrong?
> >
> > Thanks,
> >
> > John
> >
> >
> > On Tuesday, September 29, 2020, 01:35:48 AM PDT, Jim Lemon
> > wrote:
> >
>
> >
> > John
> >
> >
> > On Tuesday, September 29, 2020, 01:35:48 AM PDT, Jim Lemon
> > wrote:
> >
> >
> >
> >
> >
> > Hi John,
> > Perhaps the most direct way would be:
> >
> > plot(fit1, col=1:2)
> >
4:41:57 PM PST, array chip via R-help
wrote:
>Dear all, I have this simple dataset to measure the yeild of a crop collected
>in 2 batches (attached). when I ran a simple inear mixed model using lmer to
>estimate within-batch and between-batch variability, the between-batch
>variabil
Hi,
I downloaded R4.0.2 and installed it succesffully without any error. However,
when I opened up a R session (using x64) and tried to install packages, I got
the following error message:
> utils:::menuInstallPkgs()
Warning: failed to download mirrors file (internet routines cannot be loaded);
PDT, array chip via R-help
wrote:
Hi,
I downloaded R4.0.2 and installed it succesffully without any error. However,
when I opened up a R session (using x64) and tried to install packages, I got
the following error message:
> utils:::menuInstallPkgs()
Warning: failed to download mirrors f
Hello everyone,
I saw this scatterplots from a paper and thought it looked very nice:
https://drive.google.com/file/d/1V7F1gq-J_GIFDOrJs00hwGyXUqCZ_xwa/view?usp=sharing
It was similar to stripchart() with 'jitter' method, but it has a special
pattern of aligning points which made it look nice
Hello everyone,
I saw this scatterplots from a paper and thought it looked very nice:
https://drive.google.com/file/d/1V7F1gq-J_GIFDOrJs00hwGyXUqCZ_xwa/view?usp=sharing
It was similar to stripchart() with 'jitter' method, but it has a special
pattern of aligning points which made it look nice
Hello,
I made a mistake today on simple counting in R, that almost got me into
trouble. After trying multiple times, I finally figured out it's rounding issue
in R.
For exmaple, when I just simply type:
> (6.9-6.3) > 0.6
[1] TRUE
6.9-6.3 should be 0.6 exactly, but R thinks that it's greater t
Thanks Richard. Got it now...
On Thursday, September 3, 2020, 10:12:36 PM PDT, Richard M. Heiberger
wrote:
FAQ 7.31
On Fri, Sep 4, 2020 at 12:47 AM array chip via R-help
wrote:
>
> Hello,
>
> I made a mistake today on simple counting in R, that almost got me into
> troubl
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