similar to: affy quality

Hi, I'm just a beginner, who has just encountered a problem! 1. - I wanted to load a csv file with names in the rows (1st column) and and numbers in the 2nd til 10th column. The file contains names in the headers. - I used; a <- as.matrix(read.table("filename", sep=',", row.names=1, header=TRUE) Question; 1 - I would like to select the first four columns 2 -

Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] "ProgressBarText" [1]

Hi, I have been using the prcomp function to perform PCA on my example microarray data, (stored in metric text files) which looks like this: 1a 1b 1c 1d 1e 1f ...................................................4r 4s 4t g1 1.2705 1.2766 ...........................................................2.0298 g2 0.1631

Hello, I have a problem with read.affy.mixed function. I want to read in together a set of CEL files from chip types Affymettrix HGU133A_2 and HGU133_Plus_2. I have my files to be read in in one directory together with a white space delimited file describing them (covdesc). In this directory I give a command: > merge <- read.affy.mixed() Error in merged[[i]] : subscript out of

Dear All, There is a question I met when using Affy package in Bioconductor. I asked it in BioC and didn't get any responses. Sorry to post again: Could anyone tell me how to draw a deep-blue Affymetrix image through Image() function in Affy package? The default settings of image() draw me a black-white image and if I modify it to 256 colors, I get a somehow yellowish image. The reason

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this automatically? Best wishes Kristian -- _____ Dr Kristian Unger Imperial College London

I would like to build a package for the HT HG-U133+ PM arrays from affy, but I can't find any good documentation on how to go about it. Naively using makecdfenv's make.cdf.package() causes R to seg-fault. I'm unfamiliar with the CDF format as such, but I'm guessing that it's changed somewhat because the PM arrays no longer have P/A and mismatches. I'm looking to build

Dear all, I was trying to normalize a subset of affy data those transcribe are either P or M (called pm_filter). I am able to normalize pm_filter subset by using RMA method, however MAS5 is not working. For RMA method, I used the following commend: est<-rma(affydata, subset=pm_filter). Could any help me; how do I do this by using MAS5 method? Regards, Anup Som -- Dr. Anup Som,

Hi , I was trying read in an affy array/matrix and then to calculate the mean value for all the duplicates. Is there a function in the R package that would do this? I tried the help function and searched for 'duplicate'. Although it provides a list of functions that would eliminate the duplicate probe ids, I couldn't find one that would calculate the mean for the duplicates. Any

Hi, folks: I have used R for some time and have not explore deep inside the codes of the packages. Today, I try to modify some code in a package of arrayQuality (I do not think it matters which package it is). There is a function called maQualityPlots and I use fix(maQualityPlots) that I can view and edit the code of this function. However, there is another function qpMAPlots that I want to edit,

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

I am attempting to develop a multiple regression model using selected model variables that should all be treated as numeric (mostly real) values. However, R considers one specific variable "mass" automatically to be of class "factor", probably because "mass" consists of integer values that are repeated. I now want to force R to treat "mass" as a numeric

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

I am hoping to get some advise on the following: I am looking for an automatic variable selection procedure to reduce the number of potential predictor variables (~ 50) in a multiple regression model. I would be interested to use the forward stepwise regression using the partial F test. I have looked into possible R-functions but could not find this particular approach. There is a function

Hi to all, very strange! I tried to debug why imap process takes 100% CPu and it is very slow when I move an email from an imap folder to another imap folder and then I typed: strace -tt -o /log-imap.txt -p <process number> well, during the trace the imap process doesn't crash and it is very fast. If I stop the tracing, I have again the problem and sometimes the crash of the

Dear All, I am analysing a dataset on levels of herbivory in seedlings in an experimental setup in a rainforest. I have seven classes/categories of seedling damage/herbivory that I want to analyse, modelling each separately. There are twenty maternal trees, with eight groups of seedlings around each. Each tree has a TreeID, which I use as the random effect (blocking factor). There are two

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Hi, i was looking into the documentation for the rma() function in affy() package, and was trying to figure out how exactly the background normalization is done. I read all three papers cited in the rma() documentation, but the most detailed explanation i could find was in Irizary et al., 2003, where they state that they compute B(PM_{ijn}) = E[s_{ijn} | PM_{ijn}] where s_{ijn} is assumed to

When I try to load cel files (hgu133a) using the ReadAffy() in R 1.8.1 command I get an error message: > x<-ReadAffy() Error: cannot allocate vector of size 102973 Kb Does anybody know what does this error mean and how to overcome it? I have tried to load the same data with R 1.7.1 and it works. There is also no error when I use R 1.8.1 to load moe430 cel files. Thanks very much for any

Hello All, I need your help. I am analysing affymetrix data and have to select the probe-set that has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of