similar to: M-value and fold change

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

Dear R user! I have a small question! I have calculated the relative importance of the variables. However I would like to compare the relative importance of two different groups of variables (i.e Strategy and industry) For example let me say that strategy has 2 sub varialbes and industry has four different variables! Can I simply add the importance of those four industry variables importance

Hi, I am really new to edge R and I have used it to calculate gene expression with RNASeq data comparing 2 different conditions. I used a P value of 0.05 and I got a list of DGE contigs up and down regulated. WhatI was wondering is how to convert the logFC value that appear in the output of the exact test. Is it a log2 base? Is fold 2 change considered as cutoff? I am trying to find this info on

Dear Prof.Thank you for your kind response. I have only used: install.packages("tidyverse") install.packages("meta") install.packages("metafor") library(tidyverse) library(meta) library(metafor)and then,forest.meta(hidemeta, layout="RevMan5", xlab="Proportion", comb.r=T, comb.f=F, xlim = c(0,1), fontsize=10, digits=3)Unfortunately I am not

Dear Fahimeh It would help if you also told us what package you are using as there are several which perform forest plots. I assume it is meta. Your plot is cropped on three side as far as I can see. What parameters did you give to the call of the graphics device? What happens if you use a different graphics format like pdf? Then we may be able to see where the issue lies. Michael On

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Hello All, I have been modifying LLVM a project of mine, and have encountered issues with overloading an intrinsic function. I have defined two types, abit (which is mapped, in Intrinsics.td, to i128) and qbit (accordingly mapped to i16). I would like my intrinsic function, CNOT(x,y), to accept either an abit or a qbit for each argument, so I overload with iAny and llvm_anyint_ty, as seemed to

Hi,when I perform SAM on my array data(siggenes)I have some problems in retrieving the separate lists of up regulated and down regulated genes. When I write: fold<-function(x){ gruppi<-split(x,controllo) geni1<-abs(mean(gruppi[[2]])-mean(gruppi[[1]])) return(geni1) } fold<-esApply(expr.contr.tratt.4,1,fold)

Hi David, The error shows that the clang source code uses this intrinsic as well, but in the old form. You need to modify the clang source code (where this intrinsic is used) to consider the overloaded operands. The assert would show the trace where clang uses this intrinsic. Hope this helps, Anna > On Jul 26, 2016, at 3:21 PM, David Noursi via llvm-dev <llvm-dev at lists.llvm.org>

Dear R users, i try to produce the fold change versus fold change plot where i have the values for x and y ranging from 0.01 to 100. So i start with plot(x,y,xlim=c(0.01,100),ylim=c(0.01,100), axes=F). Then i would like both axes to have tick marks as c(0.01,0.1,1,10,100) but they should appear equidistant. How should i manage this? Thank you for your help, Alla.

Dear all, I am reading the book "statistic analysis of gene expression microarray data" by Terry Speed . On page16-17, there is an example that I can not repeat. The content can be found using below linkage:

So I have one of these, that I bought cheap on eBay. It was working just fine on my main -STABLE workstation (Abit KG7 motherboard), up until last Friday when I moved it onto the VIA EPIA-M machine I'm building. The NIC was detected OK as aue0, then the machine locked up running dhclient. It turns out that it wasn't really hung, but apparently spinning in the kernel on behalf of

Hi , I have built decision tree using rpart . I want to do k Fold validation on the decision tree . Could you help how can i do that .. please tell the package which required for K fold validation. Regards, Santosh -- View this message in context: http://r.789695.n4.nabble.com/Need-Help-in-K-fold-validation-in-Decision-tree-tp4630730.html Sent from the R help mailing list archive at

Fold in Mathematica (or reduce in Python) works as follows: Fold[f, x, {a, b, c}] := f[f[f[x,a],b],c] That is, f is a binary operator, x is the initial value, and the results are cascaded along the list. I've found it useful for reducing lists when I only have a function that accepts two arguments (e.g., merge in R). Is there any R equivalent? I'm a newbie in R and having a hard

I was trying to install CentOS 6.4 a workstation with an Abit AB9 motherboard on a machine that had been running 5.9 Installation completed, but upon boot, it hangs hard after acpiphp: ACPI Hot Plug PCI Controller Driver version 0.5 ipmi message handler version 39.2 ? then 3 attempts to locate an ipmi interface at different addresses ... Refined TSC clocksource calibration: 2175.999 MHz

Hi, I was trying to get the optimal 'k' for the knn. To do this I was using the following function : knn.cvk <- function(datmat, cl, k = 2:9) { datmatT <- (datmat) cv.err <- cl.pred <- c() for (i in k) { newpre <- as.vector(knn.cv(datmatT, cl, k = i)) cl.pred <- cbind(cl.pred, newpre) cv.err <- c(cv.err, sum(cl != newpre)) }

Hi all, Has anyone tried to do k-fold cross validation for flexible discriminant analysis ( mda library), for example, using crossval() in bootstrap? The problem is that the function crossval() requires a separate matrix for predictors and another for responses, whereas the function fda(), using the formula argument only. Is there another way of doing k-fold cross validation for functions which

Hi, I am using the Random Forest package to classify observations into one of two classes. My data is unbalanced with the minority class accounting for 7% of total data set. I have heard the 10-Fold Cross validation can help me with improving classification. But being new at most of this it's not something I can do from scratch on my own. So I have spent all this morning trying to find a

Add a specific optimisation pass for NV50 to check whether SRC0 or SRC1 is a MOV dst, IMM. If so: fold the IMM in and try to drop the MOV. Must be done post-RA because it is required that SDST == SSRC2. Signed-off-by: Roy Spliet <rspliet at eclipso.eu> --- .../drivers/nouveau/codegen/nv50_ir_peephole.cpp | 52 ++++++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git

Add a specific optimisation pass for NV50 to check whether SRC0 or SRC1 is a MOV dst, IMM. If so: fold the IMM in and try to drop the MOV. Must be done post-RA because it requires that SDST == SSRC2. V2: improve readability and add comments to clarify decisions Signed-off-by: Roy Spliet <rspliet at eclipso.eu> --- .../drivers/nouveau/codegen/nv50_ir_peephole.cpp | 60