search for: muscles

...quot; "LOC100047324///Sesn1" "1416926_at" "3.19e-10" "2.172342" "Trp53inp1" "1422557_s_at" "1.58e-09" "2.9569254" "Mt1" etc. using the following code: muscle = read.table(file="/Users/bob/Desktop/Muscle/musclesmall.txt", header = TRUE, colClasses = "character", fill = TRUE) upregulated_list = c() downregulated_list = c() nochange = c() p_thresh = 6.51e-06 x=1 while (x <= nrow(muscle)) { this_pval = muscle[x,"adj.P.Val"] this_M = muscle[x, "logFC"] if (muscle[x, &qu...

Hi everyone,  I am using bio3d package for some sequence analysis because of its nice integrated MUSCLE execution. However, I have been encountering some errors while I was running seqaln function, which calls for installed MUSCLE program. In my case, I stored the MUSCLE program on the desktop with pathway of "./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from

I would like to plot 3-dimensional data on a two-dimensional scatter-plot. Is there a way I can automatically modify the plot symbol (e.g. changing size or color) to indicate the value of a third variable? E.g. How can I plot weight vs. age and indicate the value of muscle mass for each value weight-age pair by making the plot point proportional to the subject's muscle mass? Thanks, John

Hi all, a modified version of the OpenSSH client programs has been released on the Smart Sign Web Site http://smartsign.sourceforge.net that uses Muscle Card Edge technology. It directly generates an OpenSSH private key on to a JavaCard 2.1.1 compliant smart card (using CardEdge key generation facility) and uses it from the card itself. Private key can never get compromised after generation !

I would appreciate help translating the following lme model to an lmer function. lme(lognrms ~ Group*Rotation*muscle*side*support*arms, random=~1|Subject/Stratum2/rep, data=Data) Many thanks Ross Darnell r.darnell at uq.edu.au

In S-Plus, I can obtain polynomial contrasts for an ordered factor with contr.poly(). The function also exists in R, however is limited to factors where the levels are equally spaced. In S-Plus, one can obtain the contrasts for a set of numeric values representing unequally spaced ordered factors. Has anyone implemented this in R? I see that the S-Plus function calls another function (poly.raw())

[cross-posted from bioc-devel list] Hi all, I have a subtle question related to how R CMD SHLIB handles variables in make child processes. In more detail: I am the maintainer of the 'msa' package which has been in Bioconductor since April 2015. This package integrates three open-source libraries for multiple sequence alignment. This is organized in the following way: in src/, there

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On Mon, May 12, 2014 at 9:34 AM, Manuel Klimek <klimek at google.com> wrote: > It seems that we cannot execute svn commands against llvm-project any more: > $ svn diff -r 208457:208458 'http://llvm.org/svn/llvm-project' > svn: access to '/svn/llvm-project/!svn/vcc/default' forbidden > > Tanja, any idea what changed? > (Tanya, sorry for messing up the name,

Hi, I have some data on the effect of cycle shape (categorical) and frequency (continuous) on the efficiency of muscle contraction. My minimum adequate model is: m15<-glm(efficiency~cycle.shape*freq, family=quasipoisson) However, I wish to know where significant differences lie between specific combinations of treatments. I guess I want an equivalent of a post hoc test following an

On Mon, May 19, 2014 at 1:48 PM, Alex Bradbury <asb at asbradbury.org> wrote: > On 12 May 2014 08:35, Manuel Klimek <klimek at google.com> wrote: > > On Mon, May 12, 2014 at 9:34 AM, Manuel Klimek <klimek at google.com> > wrote: > >> > >> It seems that we cannot execute svn commands against llvm-project any > >> more: > >> $ svn

Dear all, I did post this more or less identical mail in a follow up to another question I posted, but under another heading. I try again, but now under the correct header. upon running this code (from the Hmisc library-latex function) I believe the call to summary.formula is allright and produces wonderful tables, but the latex command results in a correct formatted table but where all the

Gday, This is a repost since I only had one direct reply and I remain mystified- This may be stupidity on my part but it may not be so simple. In brief, my problem is I'm not sure how to extract parameter values/effect sizes from a nonlinear regression model with a significant interaction term. My data sets are dose response curves (force and dose) for muscle that also have two

Hello forum! As the subject indicates, I am trying to make a barplot and would like my column names to be in bold. Is this possible in R without having to make my column names in mtext? Any help would be much appreciated. The code I am using is as follows. par(mar=c(3,8,2,2)) par(adj=.5) par(font=2) par(oma=c(3,3,3,3)) par(xpd=TRUE) Blot<-matrix(c(25.2995, 0.7625, 25.6135, 36.5770,

I'm wondering if anyone can give some basic advice about how to approach a specific task in R. I'm new to R but have used SAS for many years, and while I can muscle through a lot of the code details, I'm unsure of a few things. Specific questions: If I have to perform a set of actions on a group of files, should I use a loop (I feel like I've heard people say to avoid looping

G'day, My problem is I'm not sure how to extract effect sizes from a nonlinear regression model with a significant interaction term. My data sets are multiple measurements of force response to an agonist with two superimposed treatments each having two levels. This is very similar to the Ludbrook example in Venables and Ripley. The experiment is that a muscle is exposed to an agonist

Anyone working with/using it? One thing that's driving me nuts is that it keeps spitting garbage into the logs (card absent or mute!!!). I just tried editing /etc/init.d/pcscd - there's *no* way to pass parms from the config file - and set the logging level to --error, and it's still doing it. Clues for the poor, to shut it up? mark

I''d like to see tab completion introduced for the commands -- while the single-character aliases are nice, tab-completing is in my muscle memory, as I suspect it is in many others, too. I''ve written a very rudimentary completion script which merely completes the command name in Bash: http://gist.github.com/445941 What are your thoughts on this? Would it be possible to get it

Dear sir/madam, I have been using R for a while now for microarray analysis, and I would like to make a "master" data frame in which I can combine information from many different sources. The basic list a genelist with 25.000 probes, then I would like to have a subcompartment with the statistical information, a subcompartment with more extensive information regarding each gene, and then

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