Hi, I am trying to filter my probes based on the quality score, but it gives me an error. I ran the script few times. It was previously working. When I try to run the script in "BeadArrayUseCases.pdf" using the demo dataset, it also gives the same error. What could be the reason? These are the commands that I am using for my dataset: data <- read.ilmn(files="MEF triangle_Sample_Probe_Profile.txt",ctrlfiles="MEF triangle_Control_Probe_Profile.txt", probeid="ProbeID", annotation="TargetID", other.columns="Detection") data.cor <- nec(data) library(illuminaMousev2.db) illuminaMousev2() ids <- as.character(rownames(data.cor)) ids2 <- unlist(mget(ids,revmap(illuminaMousev2ARRAYADDRESS), ifnotfound=NA)) qual <- unlist(mget(ids2,illuminaMousev2PROBEQUALITY, ifnotfound=NA)) This is the error: "Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs" Here is the session info: R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] illuminaHumanv2.db_1.16.0 org.Hs.eg.db_2.8.0 [3] BiocInstaller_1.8.3 illuminaMousev2.db_1.16.1 [5] org.Mm.eg.db_2.8.0 RSQLite_0.11.2 [7] DBI_0.2-5 AnnotationDbi_1.20.3 [9] Biobase_2.18.0 BiocGenerics_0.4.0 [11] limma_3.14.3 loaded via a namespace (and not attached): [1] AnnotationForge_1.0.3 IRanges_1.16.4 parallel_2.15.2 [4] stats4_2.15.2 tools_2.15.2 Thank you, Gaye ------------------------------- This e-mail and any attachments are only for the use of the intended recipient and may be confidential and/or privileged. If you are not the recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person as it may be an offence under the Official Secrets Act. ------------------------------- [[alternative HTML version deleted]]

Hi Gaye, Unfortunately, it looks as though this version of the illuminaHumanv2.db package has some missing probe mappings, which is causing you to get some NA values when you do the first lookup. The packages will have to be re-built and uploaded, which will take a day or so. For now, you can add an explicit check for NA values before you look up the probe qualities. ids2 <- unlist(mget(ids, revmap(illuminaHumanv2ARRAYADDRESS), ifnotfound=NA)) ids2 <- ids2[-whichis.na(ids2))] qual <- unlist(mget(ids2, illuminaHumanv2PROBEQUALITY, ifnotfound=NA)) table(qual) AveSignal = rowMeans(maqc.norm$E[as.character(names(ids2)),]) boxplot(AveSignal~ qual) rem <- qual == "No match" | qual == "Bad" maqc.norm.filt <- maqc.norm[unlist(mget(names(qual)[!rem], illuminaHumanv2ARRAYADDRESS)),] Sorry for the inconvenience, Mark On Mon, Jan 14, 2013 at 6:40 AM, Gaye SAGINC (GIS) <sagincg99 at="" gis.a-star.edu.sg=""> wrote: > Hi, > > I am trying to filter my probes based on the quality score, but it gives me an error. I ran the script few times. It was previously working. When I try to run the script in "BeadArrayUseCases.pdf" using the demo dataset, it also gives the same error. What could be the reason? > > > These are the commands that I am using for my dataset: > > data <- read.ilmn(files="MEF triangle_Sample_Probe_Profile.txt",ctrlfiles="MEF triangle_Control_Probe_Profile.txt", > probeid="ProbeID", annotation="TargetID", other.columns="Detection") > data.cor <- nec(data) > library(illuminaMousev2.db) > illuminaMousev2() > ids <- as.character(rownames(data.cor)) > ids2 <- unlist(mget(ids,revmap(illuminaMousev2ARRAYADDRESS), > ifnotfound=NA)) > qual <- unlist(mget(ids2,illuminaMousev2PROBEQUALITY, > ifnotfound=NA)) > > This is the error: > "Error in .checkKeysAreWellFormed(keys) : > keys must be supplied in a character vector with no NAs" > > Here is the session info: > R version 2.15.2 (2012-10-26) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] illuminaHumanv2.db_1.16.0 org.Hs.eg.db_2.8.0 > [3] BiocInstaller_1.8.3 illuminaMousev2.db_1.16.1 > [5] org.Mm.eg.db_2.8.0 RSQLite_0.11.2 > [7] DBI_0.2-5 AnnotationDbi_1.20.3 > [9] Biobase_2.18.0 BiocGenerics_0.4.0 > [11] limma_3.14.3 > > loaded via a namespace (and not attached): > [1] AnnotationForge_1.0.3 IRanges_1.16.4 parallel_2.15.2 > [4] stats4_2.15.2 tools_2.15.2 > > > Thank you, > > Gaye > > ------------------------------- > This e-mail and any attachments are only for the use of the intended recipient and may be confidential and/or privileged. If you are not the recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person as it may be an offence under the Official Secrets Act. > ------------------------------- > > [[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