Question: Agi4x44PreProcess for miRNA data
0
10.8 years ago by
Pedro Lopez-Romero120 wrote:
The function read.AgilentFE has not been designed to directly read data from miRNA. The error message you get is due to the fact that I included on purpose a stop point if the "Sequence and chr_coord" cannot be found in the input data set, in order to avoid using the function to read other data different from the one that the function is expecting to get. You can use this function, instead, which is similar to read.AgilentFE : read.microRNA.AgilentFE <- function(targets){ if (!is(targets, "data.frame")){ stop("'targets' must be a data.frame") } ddaux=read.maimages(files=targets$FileName,source="agilent", other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", ChrCoord="chr_coord", BGKmd="gBGMedianSignal", BGKus="gBGUsed"), columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", Rb="gMeanSignal", Gb="gProcessedSignal"), verbose=T,sep="\t",quote="") dd=new("RGList") dd$R=ddaux$R dd$G=ddaux$G dd$Rb=ddaux$Rb dd$Gb=ddaux$Gb dd$targets=ddaux$targets dd$genes=ddaux$genes[,c(4,5,6)] dd$other=ddaux$other rm(ddaux) cat("","\n") cat(" RGList:","\n") cat(" dd$R: 'gTotalGeneSignal' ","\n") cat(" dd$G: 'gTotalProbeSignal' ","\n") cat(" dd$Rb: 'gMeanSignal' ","\n") cat(" dd$Gb: 'gProcessedSignal' ","\n") cat("","\n") return(dd) } # end function HTH pedro Hi all, is there any way to get the Agi4x44PreProcess package working with Agilent miRNA data? I have a target object pointing at Agilent txt files containing miRNA data. Reading mRNA data is no problem. For miRNA data I get the following error: > dd=read.AgilentFE(targets, makePLOT=FALSE) Read ***.txt Read ***.txt ... INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = FALSE) : the script will stop now Any suggestions? [[alternative HTML version deleted]] mirna agi4x44preprocess • 510 views ADD COMMENTlink modified 10.7 years ago by MartenJäger40 • written 10.8 years ago by Pedro Lopez-Romero120 Answer: Agi4x44PreProcess for miRNA data 0 10.7 years ago by MartenJäger40 MartenJäger40 wrote: Hi Yong, hi Petro, thanks for your replies. I did as Yong suggested. Removed the stop point for "Sequence and chr_coord" and additionally set "dd$genes=ddaux$genes[,c(4:8)]" like Petro said. This way the data reading works. Unfortunately the mapping (due to a missing annotation database) as the filtering doesn't work (I know that this isn't the right annotation package): > ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, + NonUnifOL = T, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, limSAT = 75, limPopnOL = 75, limNonUnifOL = 75, + limNAS = 100, makePLOT = F, annotation.package = "mgug4122a.db", flag.counts = T, targets) FILTERING PROBES BY FLAGS FILTERING BY ControlType FLAG Error in data.frame(PROBE_ID, as.character(probe.chr), as.character(probe.seq), : arguments imply differing number of rows: 11540, 0 So I tried to modify the line in the source code by removing all sequence related lines in the "write.control.out"-function: ... #probe.seq=ddFILT$genes$Sequence ... result=data.frame(PROBE_ID,as.character(probe.chr), as.character(GENE_ID), as.character(gene.sym),as.character(gene.num), as.character(gene.des),values) colnames(result)=c("PROBE","Probe Chr-Coord", "ACCNUM","SYMBOL","ENTREZID","DESCRIPTION",paste(g2,g1,sep=" - ")) ... But I still get the above error. Did I miss something or did I look in the wrong function? Thanks. Marten > The function read.AgilentFE has not been designed to directly read data > from > miRNA. The error message you get is due to the fact that I included on > purpose a stop point if the "Sequence and chr_coord" cannot be found in > the > input data set, in order to avoid using the function to read other data > different from the one that the function is expecting to get. You can use > this function, instead, which is similar to read.AgilentFE : > > read.microRNA.AgilentFE <- function(targets){ > if (!is(targets, "data.frame")){ > stop("'targets' must be a data.frame") > } > ddaux=read.maimages(files=targets$FileName,source="agilent", > other.columns=list(IsGeneDetected="gIsGeneDetected", > IsSaturated="gIsSaturated", > IsFeatNonUnifOF="gIsFeatNonUnifOL", > IsFeatPopnOL="gIsFeatPopnOL", > ChrCoord="chr_coord", > BGKmd="gBGMedianSignal", > BGKus="gBGUsed"), > columns=list(Rf="gTotalGeneSignal", > Gf="gTotalProbeSignal", > Rb="gMeanSignal", > Gb="gProcessedSignal"), > verbose=T,sep="\t",quote="") > dd=new("RGList") > dd$R=ddaux$R > dd$G=ddaux$G > dd$Rb=ddaux$Rb > dd$Gb=ddaux$Gb > dd$targets=ddaux$targets > dd$genes=ddaux$genes[,c(4,5,6)] > dd$other=ddaux$other > rm(ddaux) > cat("","\n") > cat(" RGList:","\n") > cat(" dd$R: 'gTotalGeneSignal' ","\n") > cat(" dd$G: 'gTotalProbeSignal' ","\n") > cat(" dd$Rb: 'gMeanSignal' ","\n") > cat(" dd$Gb: 'gProcessedSignal' ","\n") > cat("","\n") > return(dd) > } # end function > > HTH > > pedro > > > > Hi all, > > is there any way to get the Agi4x44PreProcess package working with Agilent > miRNA data? I have a target object pointing at Agilent txt files > containing miRNA data. Reading mRNA data is no problem. For miRNA data I > get the following error: > >> dd=read.AgilentFE(targets, makePLOT=FALSE) > Read ***.txt > Read ***.txt > ... > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > SCANN THE DATA USING AFE 9.5.3.1 > Error in read.AgilentFE(targets, makePLOT = FALSE) : > the script will stop now > > Any suggestions? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
Hi Marten, Please, be aware that you cannot plug the microRNA data into the Agi4x44PreProcess functions, since these functions have been written for the processing of mRNA data. If you want to use the Agi4x44Preprocess, you will have to figure out by yourself the modifications that you need to do in these functions according to your data, or write a complete set of new functions. Some of the Agi4x44PreProcess functions might be useful with no modification at all, but I am afraid that this will happen only with a very few of them. p.- On Wed, Mar 11, 2009 at 4:47 AM, Marten Jäger <marten.jaeger@charite.de>wrote: > Hi Yong, hi Petro, > > thanks for your replies. I did as Yong suggested. Removed the stop point > for "Sequence and chr_coord" and additionally set > "dd$genes=ddaux$genes[,c(4:8)]" like Petro said. This way the data reading > works. > Unfortunately the mapping (due to a missing annotation database) as the > filtering doesn't work (I know that this isn't the right annotation > package): > > > > ddFILT = filter.probes(ddNORM, control = TRUE, wellaboveBG = TRUE, > isfound = TRUE, wellaboveNEG = TRUE, sat = TRUE, PopnOL = TRUE, > + NonUnifOL = T, nas = TRUE, limWellAbove = 75, limISF = 75, limNEG = 75, > limSAT = 75, limPopnOL = 75, limNonUnifOL = 75, > + limNAS = 100, makePLOT = F, annotation.package = "mgug4122a.db", > flag.counts = T, targets) > FILTERING PROBES BY FLAGS > > > FILTERING BY ControlType FLAG > Error in data.frame(PROBE_ID, as.character(probe.chr), > as.character(probe.seq), : > arguments imply differing number of rows: 11540, 0 > > > So I tried to modify the line in the source code by removing all sequence > related lines in the "write.control.out"-function: > > ... > #probe.seq=ddFILT$genes$Sequence > ... > result=data.frame(PROBE_ID,as.character(probe.chr), > as.character(GENE_ID), > as.character(gene.sym),as.character(gene.num), > as.character(gene.des),values) > colnames(result)=c("PROBE","Probe Chr-Coord", > "ACCNUM","SYMBOL","ENTREZID","DESCRIPTION",paste(g2,g1,sep=" - ")) > > ... > > But I still get the above error. Did I miss something or did I look in the > wrong function? > > Thanks. > > Marten > > > > The function read.AgilentFE has not been designed to directly read data > > from > > miRNA. The error message you get is due to the fact that I included on > > purpose a stop point if the "Sequence and chr_coord" cannot be found in > > the > > input data set, in order to avoid using the function to read other data > > different from the one that the function is expecting to get. You can use > > this function, instead, which is similar to read.AgilentFE : > > > > read.microRNA.AgilentFE <- function(targets){ > > if (!is(targets, "data.frame")){ > > stop("'targets' must be a data.frame") > > } > > ddaux=read.maimages(files=targets$FileName,source="agilent", > > other.columns=list(IsGeneDetected="gIsGeneDetected", > > IsSaturated="gIsSaturated", > > IsFeatNonUnifOF="gIsFeatNonUnifOL", > > IsFeatPopnOL="gIsFeatPopnOL", > > ChrCoord="chr_coord", > > BGKmd="gBGMedianSignal", > > BGKus="gBGUsed"), > > columns=list(Rf="gTotalGeneSignal", > > Gf="gTotalProbeSignal", > > Rb="gMeanSignal", > > Gb="gProcessedSignal"), > > verbose=T,sep="\t",quote="") > > dd=new("RGList") > > dd$R=ddaux$R > > dd$G=ddaux$G > > dd$Rb=ddaux$Rb > > dd$Gb=ddaux$Gb > > dd$targets=ddaux$targets > > dd$genes=ddaux$genes[,c(4,5,6)] > > dd$other=ddaux$other > > rm(ddaux) > > cat("","\n") > > cat(" RGList:","\n") > > cat(" dd$R: 'gTotalGeneSignal' ","\n") > > cat(" dd$G: 'gTotalProbeSignal' ","\n") > > cat(" dd$Rb: 'gMeanSignal' ","\n") > > cat(" dd\$Gb: 'gProcessedSignal' ","\n") > > cat("","\n") > > return(dd) > > } # end function > > > > HTH > > > > pedro > > > > > > > > Hi all, > > > > is there any way to get the Agi4x44PreProcess package working with > Agilent > > miRNA data? I have a target object pointing at Agilent txt files > > containing miRNA data. Reading mRNA data is no problem. For miRNA data I > > get the following error: > > > >> dd=read.AgilentFE(targets, makePLOT=FALSE) > > Read ***.txt > > Read ***.txt > > ... > > INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord > > SCANN THE DATA USING AFE 9.5.3.1 > > Error in read.AgilentFE(targets, makePLOT = FALSE) : > > the script will stop now > > > > Any suggestions? > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > [[alternative HTML version deleted]]