similar to: Searching for packages for normalizing Metabolomic data

Dear all, I've installed R-2.12.2 on a server with Suse 10 linux OS. When I try to create images I got this error: > png(filename="hola.png") Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, : unable to start device PNG In addition: Warning message: In png(filename = "hola.png") : no png support in this version

Hi!! I am a new user of R (just trying to analysis microarrays with some packages from the bioconductor project). I would like to import a text-delimeted file containing 20 columns and 22200 rows. I have tried read.table; scan(file="") <matrix(scan("file", n=20*200,20,200, byrow=TRUE)); Doesn't matter what I try I got the next message: error in file (file

Hi, I am doing a binomial GLMM with a random intercept using the formula below, but I always get the same warning message. > m01 <- lmer(pres~ HT + DN + dtree + DNm + cmnhi + cmxes + cplan + craan + lfphal0100 + lfov0100 + lfop0100 + (1|plot), family=binomial, data=vphal, verbose=TRUE) 0: 6309.9448: 0.459924 -5.20747 -0.378722 0.558779 -0.200922 -0.0488451 -0.397844 0.367916 -2.09820

Hi, I want to be able to rename a folder using R, similar to file.rename. I want to paste " - done" onto the folder name. The reason for this is we run a loop on a large number of folders on a server and it would be nice for people to be able to log in and instantly see if their data has been processed so they can remove it. I have searched the help list but have not found anything and

Hi, I'm plotting PDFs and have a problem. If I have more than 8 sources of data the colours are repeated. These plots are used to remove poor data from the sets so it would be helpful if I could expand the colour range. Is there any way to do this? The plots are coloured by defining a vector colsVec<-1:(length(mzXMLfiles)) And defined in the loop for (file in 1:length(mzXMLfiles)) as

Hey all, I''m wondering how people are using acts_as_taggable. Two things I''d like to do that aren''t supported out of the box are tag normalization and user attribution. I can''t imagine I''m the first to think about doing this. >From a schema perspective these things both seem simple, just put the normalized tag in the tags table, and have a join

To run my data in another program my data cannot exceed a kurtosis of 0.8. I'm wondering if there is a package that can determine if the kurtosis for a trait is equal to or greater than 0.8 and then determine the appropriate normalizing methods to reduce the kurtosis to less than 0.8. I would also need to have record of what normalizing procedures were done for each trait Katherine Willmore

Hi I am writing some functionality for a multivariate PDF. One problem is that evaluating the normalizing constant (NC) is massively computationally intensive [one recent example took 4 hours and bigger examples would take much much longer] and it would be good allow for this in the design of the package somehow. For example, the likelihood function doesn't need the NC but (eg) the

Hi, I have a plot whole tick values along the axis have a certain range 0 - x . I need to normalize this range without changing my data files. for e.g., if my plot has tick values at 10,20,30,40,50... i have to make this 2,4,6, etc. but without changing the plot data... I am hoping I can add something to the plot command that goes like tick values divided by a quantity. Any help is appreciated.

I am wondering if it possible to normalize the slope of a linear regression to its intercept to allow for valid between-group comparisons. Here is the scenario: I need to compare the slopes of biomass increase among NAFO divisions of Northwest Atlantic cod. However, the initial division biomass is a confounding factor that may influence the slope of the regression model. How can I normalize the

Hey all, I've been googling trying to find a tool that I can use to normalize a directory full of WAV files. I found a reference to normalize in the atrpms repo but it wants to clobber several of the base rpms. Does anyone know of a tool in CentOS 6 that can normalize a directory full of WAV files that I can install without hosing up my system? -- _ ?v? /(_)\ ^ ^ Mark LaPierre

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of

Dear list I have a large data frame with house prices. Prices have been converted to price per m2, to be able to compare. Prices are spread over almost 10 years, each price is tagged with the year it relates to. I would like to 'normalize' all the prices to, eg. 2010 prices. The data frame looks like this > head(dafP) Y P 1 2004 11199.60 2 2005 15310.10 3 2005 19491.50 4

 Hello everyone, Apologies in advance, as this is partially a stats question and partially an R question.  I have been using a GAM to model the activity level of bats going into and coming out from a forested edge.  I had eight microphones set up in a line transect at each of eight sites, and I am hoping to construct a model for each of 7 species.  My count data has a reverse J-shaped skew and

Hi, Can someone tell me how to normalize a data set so that the mean of the set is 0 and the variance is 1. As I understand, when you calculate the principle components of a data set through correlation as < princomp( dataset, cor=T ) > then a similar calculation is performed. I would like to know how I can perform such a calulation directly. Any help would be greatly appreciated. Many

Dear all, My company located in Innsbruck, Austria, has an opening for a biostatistician. If you have any interest, feel free to contact me or Dr Markus Speiser (markus.speiser*at*biocrates.com). Best regards, David ################## Biostatistician (m/f) Job Description BIOCRATES Life Sciences AG is a leading metabolomics company using a mass-spectrometry based technology

Hi, I'm working on my dial plan and I'd like to parse all dialed numbers to convert them to the format I want. For example if someone dials 0112345678 or 0033112345678 I would like to convert it to +33112345678 and then match the number to my exten => +33XXXXXXXX statements. Is this possible with asterisk? I tried different ways (using _., s, ...) but I can't seem to get that

Hello, I have a data set of about 300.000 measurements made by an STM which should apporximately fix a normal (Gaussian) distribution. I have imported the data in R and used plot(density()) to get a nice plot of the distribution which in fact looks like a real Gaussian. However, the integral over the surface is not equal to one (I know since some of the plots extend to numbers greater then 1). Is

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Hi I am a newbie to R but have tried a number of ways in R to do this and can't find a good solution. (I could do it out of R in perl or awk but would like to know how to do this in R). I have a large data frame 49 variables and 7000 observations however for simplicity I can express it in the following data frame Base, Image, LVEF, ES_Time A, 1, 4.32, 0.89 A, 2, 4.98, 0.67 A, 3, 3.7, 0.5