Error by using gpr data with marray
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@guest-user-4897
Last seen 6.6 years ago
hi, I am just a beginner in using R and bioconductor. I have a microarray experiment from the arrayexpress database. http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-109 There are given the target txt and row data (gpr). Now i want used bioconductor to generate a nomalized intensity matrix for all knockout experiments. I thought i have to use limma package and tried to read the data with marray function read.GenePix but there is still an error. Then I tried to read the info txt but there is still an error too. Maybe i just chose the wrong package for my dataset. Unfortunately I don't have a clue how i can generate the normalized datamatrix but the autors of the dataset wrote thez generate the log_fold_change matrix with Imfit limma function. So i thought there is a possibility for me. please help -- output of sessionInfo(): library(limma) library(marray) read.GenePix("3088.gpr") > Error in if (skip > 0L) readLines(file, skip) : > missing value where TRUE/FALSE needed a.target <- read.marrayInfo("E-MTAB-109.sdrf.txt") > Error in names(x) <- value : > 'names' attribute [30] must be the same length as the vector [7] -- Sent via the guest posting facility at bioconductor.org.
limma marray ArrayExpress limma marray ArrayExpress • 1.2k views
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@wolfgang-huber-3550
Last seen 16 days ago
EMBL European Molecular Biology Laborat…
Dear Sandra in principle, this should work: library("ArrayExpress") a = ArrayExpress("E-MTAB-109") I just tried this. An object with data was constructed (a list of NChannelSets). However, errors and warnings were thrown. The resulting datastructure was more messy than it should be, and the metadata was dropped. I'll chase this up with the package maintainer and with the EBI people. You can try to read to the files provided by EBI 'manually' using limma's read.maimages etc., but for this you will need to twiddle with function call parameters and file formats, and for this you might be best off recruiting a local R expert. Best wishes Wolfgang Sandra Heise [guest] scripsit 03/09/2012 11:19 AM: > > hi, > I am just a beginner in using R and bioconductor. I have a microarray experiment from the arrayexpress database. > > http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-109 > > There are given the target txt and row data (gpr). Now i want used > bioconductor to generate a nomalized intensity matrix for all knockout experiments. I thought i have to use limma package and tried to read the data with marray function read.GenePix but there is still an error. Then I tried to read the info txt but there is still an error too. Maybe i just chose the wrong package for my dataset. Unfortunately I don't have a clue how i can generate the normalized datamatrix but the autors of the dataset wrote thez generate the log_fold_change matrix with Imfit limma function. So i thought there is a possibility for me. > > please help > > -- output of sessionInfo(): > > library(limma) > library(marray) > > read.GenePix("3088.gpr") > >> Error in if (skip> 0L) readLines(file, skip) : >> missing value where TRUE/FALSE needed > > a.target<- read.marrayInfo("E-MTAB-109.sdrf.txt") > >> Error in names(x)<- value : >> 'names' attribute [30] must be the same length as the vector [7] > > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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