User: Guoneng Zhong

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Guoneng Zhong180
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Posts by Guoneng Zhong

<prev • 18 results • page 1 of 2 • next >
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merging fit and MA objects
... Hi, Is there an easy way to merge data from a fit object (from lmFit) and MA data (from normalizeWithinArrays) based on the genes? I mean, I want the p values from the fit object and the different M values (each column represents an original file), matching the data based on fit$gene or MA$gene. ...
written 14.0 years ago by Guoneng Zhong180
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writing weight function
... Hi, Has anyone written a weight function to be used with limma's read.maimages()? I tried this (based on typing wtflag): wtblank <- function(w=0.1) function(gpr){ flagged <- (gpr[,"ID"] = "BLANK") w * flagged + (!flagged) } And here are the errors I got from two differen ...
written 14.3 years ago by Guoneng Zhong180
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ignore blanks in GPR
... Hi, In limma, how do I read a GPR file and ignore any lines whose ID column is BLANK or ""? This is my line: RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf="F635 Median",Rb="B635 Median")) Thanks! G ...
limma written 14.3 years ago by Guoneng Zhong180 • updated 14.3 years ago by Lourdes Peña Castillo140
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ebayes giving warning, should I trust the result?
... Hi, Here is my code (thanks to all those who helped me with getting the columns right). library(limma) targets <- readTargets('targets.txt') f <- function(x) as.numeric(x$Flags > -99) RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf ...
written 14.5 years ago by Guoneng Zhong180 • updated 14.5 years ago by Gordon Smyth39k
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eBayes giving warning, should I trust the result?
... Hi, Here is my code (thanks to all those who helped me with getting the columns right). library(limma) targets <- readTargets('targets.txt') f <- function(x) as.numeric(x$Flags > -99) RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf ...
written 14.5 years ago by Guoneng Zhong180
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Answer: A: limma reading wrong column for GPR files
... The version of limma is 1.9.4 and the R command I executed was: library(limma) targets <- readTargets('targets.txt') f <- function(x) as.numeric(x$Flags > -99) RG<-read.maimages(targets$FileName,source="genepix",wt.fun=f) When I typed RG, it shows that the Rf reading for the first row ...
written 14.5 years ago by Guoneng Zhong180
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limma reading wrong column for GPR files
... Hi, I have files generated by Genepix 3.0 and when I use maimages (source="genepix") and checked the RG value (RG being the object created by read.maimages), the red channel foreground reading and the greenchannel foreground reading are swapped (incorrectly), but the background channel are not swa ...
limma written 14.5 years ago by Guoneng Zhong180 • updated 14.5 years ago by michael watson IAH-C3.4k
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Unable to read GPR files for LIMMA
... Hi, read.maimages seems to be fine reading five GPR (1.3) files. But when I tried to correct for backgrond, I get this: RG <- backgroundCorrect(RG,method='normexp') Corrected array 1 Corrected array 2 Corrected array 3 Corrected array 4 Error in optim(c(beta, log(sigma), log(alpha)), sumlogli ...
normalization written 14.5 years ago by Guoneng Zhong180
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LIMMA: how to assign file name
... Hi, In limma there is this plot function: plotMA3by2 It's great. But it doesn't seem to allow me to assign a file name. And it ignores any jpeg or other device calls before it where i could assign a filename. It is writing to the current directory, which I have no write privelege to. So any id ...
limma assign written 14.5 years ago by Guoneng Zhong180 • updated 10 months ago by Bioconductor Community ♦♦ 0
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saving graphs
... Hi, How would I save the graphing results of, say, plotMA(fit) from limma to some jpeg/gif file? Thanks, g ...
written 14.5 years ago by Guoneng Zhong180 • updated 14.5 years ago by michael watson IAH-C3.4k

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