## User: Guoneng Zhong

Guoneng Zhong180
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13 years, 10 months ago
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14 years, 10 months ago
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g************@yale.edu

#### Posts by Guoneng Zhong

<prev • 18 results • page 1 of 2 • next >
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... 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 13.8 years ago by Guoneng Zhong180
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... 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 14.2 years ago by Guoneng Zhong180
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... 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$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf="F635 Median",Rb="B635 Median")) Thanks! G ... written 14.2 years ago by Guoneng Zhong180 • updated 14.2 years ago by Lourdes Peña Castillo140 1 answer 736 views 1 answer ... Hi, Here is my code (thanks to all those who helped me with getting the columns right). library(limma) targets <- readTargets('targets.txt') f <- function(x) as.numeric(x$Flags > -99) RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf ... written 14.3 years ago by Guoneng Zhong180 • updated 14.3 years ago by Gordon Smyth38k 0 answers 499 views 0 answers ... Hi, Here is my code (thanks to all those who helped me with getting the columns right). library(limma) targets <- readTargets('targets.txt') f <- function(x) as.numeric(x$Flags > -99) RG<-read.maimages(targets$FileName,source="genepix",columns=list(Gf="F 532 Median",Gb="B532 Median",Rf ... written 14.3 years ago by Guoneng Zhong180 3 answers 558 views 3 answers ... The version of limma is 1.9.4 and the R command I executed was: library(limma) targets <- readTargets('targets.txt') f <- function(x) as.numeric(x$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 14.3 years ago by Guoneng Zhong180
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... 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 ...
written 14.3 years ago by Guoneng Zhong180 • updated 14.3 years ago by michael watson IAH-C3.4k
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... 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 ...
written 14.3 years ago by Guoneng Zhong180
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... 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 ...
written 14.4 years ago by Guoneng Zhong180 • updated 8 months ago by Bioconductor Community ♦♦ 0
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... Hi, How would I save the graphing results of, say, plotMA(fit) from limma to some jpeg/gif file? Thanks, g ...
written 14.4 years ago by Guoneng Zhong180 • updated 14.4 years ago by michael watson IAH-C3.4k

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