I have a custom affy chip (dont know what more information would be relevant here (I am new to this)). I am attempting to perform background correction using the bg.correct.mas function and am running into problems because of na values in a very small (5 or so) number of the mm values (At least, I think this is why I am running into problems). First, I noticed that none of the bg.correct.*, normalize.* methods have an na.rm parameter - this seems to indicate to me that having NA values in pm, mm matrices is not expected and therefore I am reading in the data incorrectly. Is this true? I took it for granted that it was not true, and have been trying to exclude them after the fact. First, to get the data into R i do: > cdf.env <- make.cdf.env("Mar_12_2004.cdf") > affybatch <- read.affybatch(filenames = c("T1.CEL")) > affybatch@cdfName <- "cdf.env" This occurs without incident (save the warning: Incompatible phenoData object. Created a new one.) So then I want to do the following: > bg.correct.mas(affybatch) Error in as.vector(data) : NA/NaN/Inf in foreign function call (arg 1) So... My first thought was to find all probesets with NA values, and then remove them from the AffyBatch object (please excuse the codes ugliness, just trying to make it work for now): remove.na.vals <- function(affybatch) { na.probesets <- NULL for (ps in probeset(affybatch)) { if is.na(sum(pm(ps))) || is.na(sum(mm(ps)))) { na.probesets <- c(na.probesets, ps@id) } } na.probesets } So using the above function I do the following: ab.probes <- probeset(affybatch, setdiff(geneNames(affybatch), remove.na.vals(affybatch))) This gives me a list of probeset objects which have no NA values in either pm or mm column. I then want create/modify the AffyBatch object to use just this probeset. I cannot set the pm, mm values because they have different dimensions. I am sure there are alternate/superior solutions to this problem. As I said before I am new to bioconductor and so potentially I am on the wrong track entirely. Some information which might be important is below, Thanks in advance. Jim R 2.0.1 bioconductor 1.5 affy_1.5.8-1 makecdfenv_1.4.8 debian 2.6 (sarge)

Sorry to respond to my own thread, but I believe I have some more insight on what is happening. From my previous post I was having some problems with some mm values which were NA. I interogated which they were and I got the following: > indexProbes(affybatch, which = "both", "02280106180000.6757_pPM_GC") $"02280106180000.6757_pPM_GC" [1] 505546 NA I have exactly 5 genes where this is true (pm = index, mm = NA). When I examined the code for make.cdf.env there is a block: if(length(mm)==0) return(cbind(pm=pm, rep(NA,length(pm)))) else return(cbind(pm=pm,mm=mm)) I put some print statements in there and the mm length is 0 for my five genes. I assumed since the code was checking and handling this case that it probably meant that NA values in the mm field were okay, but now I am not sure that I can say either way. On a possibly related note, I realized that the cbind was giving me many warnings saying that the lengths of the columns dont match, ie: 1: number of rows of result is not a multiple of vector length (arg 2) in: cbind(pm = pm, mm = mm) This occurrs in the cbind above for a fair number of the probesets. I had assumed (again probably incorrectly) that because the code wasnt even checking to see if they were same length that these were *ignorable* warnings. Now, upon typing that thought I realize that it is probably the opposite, but I am pretty sure I dont know enough about cdf files to say what this indicates, and how I can correct the problem. thanks again, jim James Bullard wrote: > > I have a custom affy chip (dont know what more information would be > relevant here (I am new to this)). I am attempting to perform > background correction using the bg.correct.mas function and am running > into problems because of na values in a very small (5 or so) number of > the mm values (At least, I think this is why I am running into problems). > > First, I noticed that none of the bg.correct.*, normalize.* methods > have an na.rm parameter - this seems to indicate to me that having NA > values in pm, mm matrices is not expected and therefore I am reading > in the data incorrectly. Is this true? I took it for granted that it > was not true, and have been trying to exclude them after the fact. > > First, to get the data into R i do: > > > cdf.env <- make.cdf.env("Mar_12_2004.cdf") > > affybatch <- read.affybatch(filenames = c("T1.CEL")) > > affybatch@cdfName <- "cdf.env" > > This occurs without incident (save the warning: Incompatible phenoData > object. Created a new one.) > > So then I want to do the following: > > > bg.correct.mas(affybatch) > Error in as.vector(data) : NA/NaN/Inf in foreign function call (arg 1) > > So... My first thought was to find all probesets with NA values, and > then remove them from the AffyBatch object (please excuse the codes > ugliness, just trying to make it work for now): > > remove.na.vals <- function(affybatch) { > na.probesets <- NULL > > for (ps in probeset(affybatch)) { > if is.na(sum(pm(ps))) || is.na(sum(mm(ps)))) { > na.probesets <- c(na.probesets, ps@id) > } > } > na.probesets > } > > So using the above function I do the following: > > ab.probes <- probeset(affybatch, setdiff(geneNames(affybatch), > remove.na.vals(affybatch))) > > This gives me a list of probeset objects which have no NA values in > either pm or mm column. I then want create/modify the AffyBatch > object to use just this probeset. I cannot set the pm, mm values > because they have different dimensions. I am sure there are > alternate/superior solutions to this problem. As I said before I am > new to bioconductor and so potentially I am on the wrong track > entirely. Some information which might be important > is below, Thanks in advance. Jim > > R 2.0.1 > bioconductor 1.5 > affy_1.5.8-1 > makecdfenv_1.4.8 > debian 2.6 (sarge) > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >