AgiMicroRna problem
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@pedro-lopez-romero-3331
Last seen 8.1 years ago
Hi Pablo, The function "read.maimages" is no longer used by AgimicroRna. "read.maimages" creates an object of class RGList with element names: R, Rb, G, Gb, etc ..., that are proper for two-channel arrays. To make the names more intuitive for the analysis of microRna arrays, I have introduced some changes and now, AgimicroRna creates an object of class uRNAlist with the names: "TGS" for the "gTotalGeneSignal", "TPS" for the "gTotalProbeSignal", "meanS" for the "gMeanSignal", "procS" for the "gProcessedSignal". If you use "read.maimages" you will create an object that is no longer available in AgimicroRna, and that´s the error you´ve got. Please, to read the data use the fucntion: readMicroRnaAFE(targets,verbose=FALSE). Please have a look at the help of readMicroRnaAFE and at the vignette file (to see the changes) For a quick look of the new characteristics of AgiMicroRna, please, have a look as well at: "Lopez-Romero P. Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library. BMC Genomics 2011, 12:64". p.- On Sun, Jan 30, 2011 at 1:03 AM, Paulo Nuin <nuin@genedrift.org> wrote: > Hi > > We're trying to analyse some Agilent microRNA chips with AgiMicroRna > without much success. Our chips are V1 and I saw in the documentation that > the package is intended to V2. Anyway, we were able to work around the > columns issue, but know we are stuck on another problem. > > Our dataset is composed of 30 chips, each one from a different sample. > Eleven of those 30 are one treatment, while the remainder 19 are in another > treatment. We created a targets file as specified by the manual with 4 > columns: > > Filename Treatment GErep Subject > fileA A 1 1 > fileB A 1 2 > fileC B 2 3 > fileD B 2 4 > .... ... ... 30 > > > We were able to read the images into a variable using > > dd=read.maimages(files=targets$FileName,source="agilent", > columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", > Rb="gTotalGeneSignal", Gb="gProcessedSignal"), > other.columns=list(IsGeneDetected="gIsGeneDetected", > IsSaturated="gIsSaturated", > IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", > probe_mappings="probe_mappings", BGKmd="gBGMedianSignal", > BGKus="gBGUsed"), annotation = c( "ControlType","ProbeName","GeneName"), > verbose=TRUE,sep="\t",quote="") > > names(dd$others) will output > > names(dd$other) > [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" > "gIsFeatPopnOL" "gBGMedianSignal" > > But when we run the rmaMicroRna with > > ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) > > we get the following error: > > Error in split.default(0:(length(pNList) - 1), pNList) : > Group length is 0 but data length > 0 > > Any help is very appreciated. > > Thanks in advance > > Paulo Nuin > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] ADD COMMENT 0 Entering edit mode Paulo Nuin ▴ 200 @paulo-nuin-3012 Last seen 7.7 years ago Canada Thanks a lot. I will try this. Cheers Paulo On 2011-02-01, at 5:00 AM, Pedro Lopez-Romero wrote: > > Hi Pablo, > > The function "read.maimages" is no longer used by AgimicroRna. > "read.maimages" creates an object of class RGList with element names: R, Rb, G, Gb, etc ..., that are proper for two-channel arrays. To make the names more intuitive for the analysis of microRna arrays, I have introduced some changes and now, AgimicroRna creates an object of class uRNAlist with the names: > "TGS" for the "gTotalGeneSignal", > "TPS" for the "gTotalProbeSignal", > "meanS" for the "gMeanSignal", > "procS" for the "gProcessedSignal". > > If you use "read.maimages" you will create an object that is no longer available in AgimicroRna, and that?s the error you?ve got. > > Please, to read the data use the fucntion: readMicroRnaAFE(targets,verbose=FALSE). > > Please have a look at the help of readMicroRnaAFE and at the vignette file (to see the changes) > For a quick look of the new characteristics of AgiMicroRna, please, have a look as well at: "Lopez-Romero P. Pre-processing and differential expression analysis of Agilent microRNA arrays > using the AgiMicroRna Bioconductor library. BMC Genomics 2011, 12:64". > p.- > > > > On Sun, Jan 30, 2011 at 1:03 AM, Paulo Nuin <nuin at="" genedrift.org=""> wrote: > Hi > > We're trying to analyse some Agilent microRNA chips with AgiMicroRna without much success. Our chips are V1 and I saw in the documentation that the package is intended to V2. Anyway, we were able to work around the columns issue, but know we are stuck on another problem. > > Our dataset is composed of 30 chips, each one from a different sample. Eleven of those 30 are one treatment, while the remainder 19 are in another treatment. We created a targets file as specified by the manual with 4 columns: > > Filename Treatment GErep Subject > fileA A 1 1 > fileB A 1 2 > fileC B 2 3 > fileD B 2 4 > .... ... ... 30 > > > We were able to read the images into a variable using > > dd=read.maimages(files=targets$FileName,source="agilent", columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", > Rb="gTotalGeneSignal", Gb="gProcessedSignal"), other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", > IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", probe_mappings="probe_mappings", BGKmd="gBGMedianSignal", > BGKus="gBGUsed"), annotation = c( "ControlType","ProbeName","GeneName"), verbose=TRUE,sep="\t",quote="") > > names(dd$others) will output > > names(dd$other) > [1] "gIsGeneDetected" "gIsSaturated" "gIsFeatNonUnifOL" "gIsFeatPopnOL" "gBGMedianSignal" > > But when we run the rmaMicroRna with > > ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) > > we get the following error: > > Error in split.default(0:(length(pNList) - 1), pNList) : > Group length is 0 but data length > 0 > > Any help is very appreciated. > > Thanks in advance > > Paulo Nuin > > _______________________________________________ > 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 >