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Hi, I applied a linear mixed effect model in my data using the nlme package. lme2<-lme(distance~temperature*condition, random=~+1|trial, data) and then anova. I want to ask if it is posible to get the least squares...

Hi, I want to ask which way is more effective to further analyse (multiple comparisons) a mixed model repeated measures anova with 2 fixed factor and 1 random? anova(lme(expr~treatment*age,random=~1|trial, data) Is searching for...

Hi all, I am getting a strange error in the check of my package recoup in the current dev branch. https://master.bioconductor.org/checkResults/3.15/bioc-LATEST/recoup It seems that the error is originated by the tests...

Hello, Indeed there seems to be a global schema change regarding external_gene_id to the latest versions of most Ensembl supported organisms which affected also my package metaseqR. One solution is to change the host in the useMart function...

Hi, I am completely new to R and I feel kind of lost. Although I can accomplish most of the basic taks, I am very confused when I am trying to do the following: I have multiple sets of 2D...

On 29/6/22 17:18, Tomas Kalibera wrote: > > Thanks, yes, could you please send a patch for R-devel? So that it is > clear which PROTECTions you have in mind, and that they haven't been > fixed already in...

Dear all, For some time now, my package metaseqR fails to pass the checks at the build system http://bioconductor.org/checkResults/3.6/bioc-LATEST/metaseqR/ Although I am not sure I understand the source of the problem (all...

Hello to all. In ggiraph package, we are getting some warnings about "Stack imbalance in NextMethod" when we subclass a primitive grob and override the widthDetails function. This started to occur from R version 4.2 onward, in various platforms...

Hi all, I would like to add also metaseqR in the list of packages failing to build in malbec1 and morelia because of vsn. What would be the most appropriate course of action for the maintainers? Wait for vsn to...

Hello, In the previous Bioconductor release (2.14), a countData object from the baySeq package could be accessed by sample names. Now it seems that it can be accessed only by indices (version 2.0.50). Was this done on...

Thank you for the very thorough explanation Paul. To answer your question on 11: The dsvg device, simply defines svg elements with their attributes (rect with fill & stroke in my examples). It does not do any internal image processing like...

Dear Kasper and Herv?, Thank you for your feedback and apologies for reviving such an old thread. Herv?, you are right, apologies for the confusion in the message title and content, it is a software package for creating/retrieving specific...

Dear developers, I maintain two packages (metaseqR, recoup) and about to submit an enhanced (but different in many points, thus a new package) version of the 1st (metaseqR2). During their course of development, maintenance and usage, these packages have somehow...

Hello, I'm trying to update ggiraph package in graphic engine v15 (currently we support up to v14). I've implemented the group operators and when I compare the outputs of ggiraph::dsvg with the outputs of svg/png, I...

Hi, sure I attach the test code and my svg. You can also find my current work on ggiraph in the branch ge15 on github: https://github.com/sigmapi/ggiraph/tree/ge15 Thanks, Panagiotis On 27/9/22 04:44...

Thank you Martin! I had missed that part. Indeed maybe you can update the instructions for non-git masters (like me). On Fri, Aug 25, 2017 at 1:14 PM, Martin Morgan < martin.morgan at roswellpark.org> wrote: > On 08...

Here is the code again in text: src <- rectGrob(2/3, 1/3, width=.6, height=.6, gp=gpar(lwd = 5, fill=rgb(0, 0, 0.9, 0.4))) dst <- rectGrob(1/3, 2/3, width=.6, height=.6, gp...

Dear all, I am facing a problem with running a script that i have written in R and i hope you can help me spot which exactly is the problem and how i can solve it. The error I get...

Dear all, I am facing a problem with running a script that i have written in R and i hope you can help me spot which exactly is the problem and how i can solve it. The error I get...