similar to: A question regarding volcano plot

Hi I am using the ggplot2 package for the volcano plot and I am using the following code for the same: g = ggplot(data=data, aes(x=data[11], y=-log10(data[12]), colour=threshold)) + + geom_point(alpha=0.4, size=1.75) + + opts(legend.position = "none") + + xlim(c(-10, 10)) + ylim(c(0, 15)) + + xlab("log2 fold change") + ylab("-log10 p-value") data[11] is a

Hello. My name is Akashah. i work at metabolic laboratory. From my study, i found that volcano plot can help a lot in my section.  i already studied about the volcano plot and get the coding to run in R software, unfortunately, there is may be something wrong with the coding. This is because  no graph appear, but no error (blue color text) was shown on the R console. Below is the coding for

Hi All, I need to calculate the median for even number of data points.However instead of calculating the arithmetic mean of the two middle values,I need to calculate their geometric mean. Though I can code this in R, possibly in a few lines, but wondering if there is already some built in function. Can somebody give a hint? Thanks in advance [[alternative HTML version deleted]]

Can't installe packag maDB or limma. Error is shown as Using R version 2.13.1, biocinstall version 2.8.4. Installing Bioconductor version 2.8 packages: Is there any other way to draw volcano plot ? Thanks [[alternative HTML version deleted]]

Folks: I know this may be overreaching, but are we missing what's important? WHY do the zeros occur? Are they values less then a known or unknown LOD? -- and/or is there positive mass on zero? In either case, using logs to calculate a geometric mean may not make sense. Paraphrasing Greg Snow, what is the scientific question? What is the model? Cheers, Bert On Mon, Jan 17, 2011 at 9:13 AM,

HELLO, anybody... could you help me to check the below coding for volcano. what is the mistake? what the plot could not display? # volcano_plot.r # # Author: Amsha Nahid, Jairus Bowne, Gerard Murray # Purpose: Produces a volcano plot # # Input: Data matrix as specified in Data-matrix-format.pdf # Output: Plots log2(fold change) vs log10(t-test P-value) # #

http://www.physorg.com/news65033298.html Switch to Rails before it''s too late, folks! Jeff -- Posted via http://www.ruby-forum.com/.

Applying the following patches closes the following task (part 1 was already taken care of). TASK: New Problems STATUS: Open FROM: <Kurt.Hornik@ci.tuwien.ac.at> New minor remarks: * The documentation for `image' still has the old order z, x, y. * Perhaps one should add `par(ask = T)' in the image demo? * Perhaps one should save the original value

Hi R-help community, Can anyone tell me why, while using : x <- seq(as.Date("2001-01-01"),as.Date("2001-01-01") + nrow(volcano)-1,1) y <- seq(1, ncol(volcano),1) when I plot the volcano matrix with that command : filled.contour(x,y,volcano) the graph has a Date format on X-axis, ok ... ... but when adding a contour plot to the filled contour, using this

Do you know what steps I need to take to add a scale to a plot? I'm pulling my example out of "An Introduction to R: Software for StatisticalModelling & Computing" (see the R code around Figure 76). I would like to add a scale to the image produced by the following code.? I would like to the scale to list the distance?and units:? data(volcano) x <- 10*(1:nrow(volcano)) y

Dear All, I was looking for the color index in?image function,?such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. ########################################### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x <- 10*(1:nrow(volcano)) y

Karline, Thank you for your help. I discovered that in addition to including clim, I needed to omit breaks. This code uses one of your other examples as a starting point and works as intended: persp3D(z = volcano, zlim = c(-60, 200), phi = 20, colkey = list(length = 0.2, width = 0.4, shift = 0.15, cex.axis = 0.8, cex.clab = 0.85), lighting = TRUE, lphi = 90, clab =

Hi list, I wonder if anyone has had this experience with squishplot() in the TeachingDemos package. Taking the example from the ?image help page, library(TeachingDemos) x <- 10*(1:nrow(volcano)) y <- 10*(1:ncol(volcano)) layout(matrix(c(1,2,3,4),ncol=2,byrow=TRUE),height=c(2,1)) ## 1st plot op <- squishplot(range(x),range(y),1) image(x, y, volcano, col = terrain.colors(100)) par(op)

Is there a way to make a shading interpolation on an image plot? Something similar to matlab 'shading interp', I think it is called Gouraud shading. What I want is to make a image plot look nicer. with image() it looks very facetted, and I would like to make it look smoother. I've tried with interp.surface() in fields package but it (obviously) makes nan values at the borders and

Hello, I would like to suggest the following change to image.default in src\library\graphics\R\image.R: 98c98 < plot(NA, NA, xlim = xlim, ylim = ylim, type = "n", xaxs = xaxs, --- > plot(x[1], y[1], xlim = xlim, ylim = ylim, type = "n", xaxs = xaxs, This provides all the support of axis.POSIXt that plot.default gives, currently the default new plot in

Hi, I am doing composite plots with the package plot3D. One of my variables is qualitative and indexed to integers, and I would like the legend for it to have labels located at the integer values (midpoints), and not at the breaks between classes. In the example below, the Elev Classes legend has labels at the breaks and nothing at the midpoints. How can I show the class labels at 1:3, and not

Hi! Whenever I save a graphic in ps/eps format generated by filled.contour or image, an undesired grid is added to it (not visible on the X11 screen). For example: postscript("volcano.eps") filled.contour(volcano,col=gray(seq(0,1,,50)),levels=seq(min(volcano),max(volcano),,50)) dev.off() Any ideia how to eliminate this grid? Thanks, Rachel [[alternative HTML version deleted]]

Hi, I wish to use R (version 2.13.1)?from within Matlab(ver R2009a) on windows XP plaform (on both 64 bit and 32 bit OS) . For this I have installed StatConnector (http://rcom.univie.ac.at/download/current/statconnDCOM.latest.exe) for calling R from within Matlab (R2009a) on Windows XP platform. I have added all the files of MATLAB_RLINK folder (downloaded from

The line contour(volcano, x, y, l, col = "yellow", lty = "solid", add = TRUE) needs to be changed to contour(x, y, volcano, col = "yellow", lty = "solid", add = TRUE) A patch is appended below. -k *** demos/graphics/graphics.orig Thu Apr 17 11:02:39 1997 --- demos/graphics/graphics Thu Apr 17 11:03:08 1997 *************** plot(numeric(0), numeric(0),

Por favor ver comentario con las las letras mayúsculas data("CPS1985", package = "AER") cps <- CPS1985 cps [1:10,] dim( cps) names( cps) library("quantreg") #regresion usual cps_lm <- lm(log(wage) ~ experience + I(experience^2) + + education, data = cps) #regresion por quantiles, tau son los cuantiles