Hello, I encounter an error while reading in gpr files with read.maimages. My codes are: f <- function(x) as.numeric(x$Flags > -50.5) RG <- read.maimages(targets, source="genepix", wt.fun=f) Error message is: Read GSM237424.gpr Read GSM237425.gpr Read GSM237426.gpr Read GSM237427.gpr Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of items to replace is not a multiple of replacement length I believe this is due to a different gpr format among some of the files. The first 4 that were read successfully are of "GenePix Result 3" type, and the next one which failed is of "GenePix Results 2" type. I checked the data, and found these versions differ in # of rows and columns. Does this mean I am unable to use Bioconductor to read + process gGenePix pr files that are of different output versions? Thanks! Casper [[alternative HTML version deleted]]

Casper Shyr scripsit 30/03/11 06:30: > > Hello, > I encounter an error while reading in gpr files with read.maimages. My codes are: > > f<- function(x) as.numeric(x$Flags> -50.5) > RG<- read.maimages(targets, source="genepix", wt.fun=f) > > Error message is: > Read GSM237424.gpr > Read GSM237425.gpr > Read GSM237426.gpr > Read GSM237427.gpr > Error in RG[[a]][, i]<- obj[, columns[[a]]] : > number of items to replace is not a multiple of replacement length > > I believe this is due to a different gpr format among some of the files. The first 4 that were read successfully are of "GenePix Result 3" type, and the next one which failed is of "GenePix Results 2" type. I checked the data, and found these versions differ in # of rows and columns. > > Does this mean I am unable to use Bioconductor to read + process gGenePix pr files that are of different output versions? Dear Casper no, but it means that you will have to write custom code, e.g., to read the different versions separately and then merge them together. There is a reason why read.maimages does not automatically read and merge files from different arrays or from different versions of the image analysis software - namely, the data may not be directly comparable and applying the standard workflow would lead to undesirable "batch effects" and silly results. I am afraid you will need to put more effort into customising your approach to importing your data and working out an appropriate analysis approach. Hope this helps Wolfgang > > Thanks! > Casper > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber