Issues with AgiMicroRna filtering step (Error in is(ddNORM, "uRNAList") : object 'ddNORM' not found)
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Karthik K N ▴ 200
@karthik-k-n-5092
Last seen 8.3 years ago
Dear mailers, I am trying to use your AgiMicroRna package to analyze my microarray data. I have created the targets files (I just have one control and one test file without any replicates). I am experiencing a problem at the filtering step and it shows the error "Error in is(ddNORM, "uRNAList") : object 'ddNORM' not found". I can not figure this out even searching for the error in different forums and manuals. I am attaching the codes that I have used. Please help me fix this issue. Thank you so much. My code is shown below: > setwd("C:/Documents and Settings/555/My Documents/miRNA") > targets.micro=readTargets(infile="targets.txt",verbose=TRUE) Target File FileName Treatment GErep B1=miRNA_1_1=Control G2 B1=miRNA_1_1=Control G2.txt C 1 B2=miRNA_1_2=Treated-G2 B2=miRNA_1_2=Treated-G2.txt Treated 2 > dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) reading file 1 - B1=miRNA_1_1=Control G2.txt reading file 2 - B2=miRNA_1_2=Treated G2.txt uRNAList: dd$TGS: 'gTotalGeneSignal' dd$TPS: 'gTotalProbeSignal' dd$meanS: 'gMeanSignal' dd$procS: 'gProcessedSignal' > qcPlots(dd.micro,offset=5, + MeanSignal=TRUE, + ProcessedSignal=FALSE, + TotalProbeSignal=FALSE, + TotalGeneSignal=FALSE, + BGMedianSignal=FALSE, + BGUsed=FALSE, + targets.micro) Error in plot.hclust(hc, labels = samples, main = "") : invalid dendrogram input > cvArray(dd.micro, + "MeanSignal", + targets.micro, + verbose=TRUE) Foreground: MeanSignal FILTERING BY ControlType FLAG RAW DATA: 15739 PROBES without CONTROLS: 15024 ---------------------------------- (Non-CTRL) Unique Probe: 2689 (Non-CTRL) Unique Genes: 939 ---------------------------------- DISTRIBUTION OF REPLICATED NonControl Probes reps 4 5 6 8 16 1512 118 59 996 4 ------------------------------------------------------ Replication at Probe level- MEDIAN CV B1=miRNA_1_1=Control G2 B2=miRNA_1_2=Treated-G2 0.285 0.270 ------------------------------------------------------ DISTRIBUTION OF REPLICATED Noncontrol Genes reps 16 939 ------------------------------------------------------ > ddTGS=tgsMicroRna(dd.micro, + half=TRUE, + makePLOT=FALSE, + verbose=FALSE) > ddNORM=tgsNormalization(ddTGS, + "quantile", + makePLOTpre=TRUE, + makePLOTpost=TRUE, + targets.micro, + verbose=TRUE) Error in plot.hclust(hc, labels = samples, main = "") : invalid dendrogram input > ddTGS.rma=rmaMicroRna(dd.micro, + normalize=TRUE, + background=TRUE) Calculating Expression > MMM=ddTGS.rma$meanS > colnames(MMM)=colnames(dd.micro$meanS) > maintitle='TGS.rma' > colorfill='blue' > ddaux=ddTGS.rma > ddaux$meanS=MMM > mvaMicroRna(ddaux,maintitle,verbose=TRUE) ------------------------------------------------------ mvaMicroRna info: FEATURES : 939 POSITIVE CTRL: 12 NEGATIVE CTRL: 7 STRUCTURAL: 3 > rm(ddaux) > RleMicroRna(MMM,"RLE TGS.rma",colorfill) > boxplotMicroRna(MMM,maintitle,colorfill) > plotDensityMicroRna(MMM,maintitle) > ddPROC=filterMicroRna(ddNORM, + dd.micro, + control=TRUE, + IsGeneDetected=TRUE, + wellaboveNEG=FALSE, + limIsGeneDetected=75, + limNEG=25, + makePLOT=FALSE, + targets.micro, + verbose=TRUE, + writeout=FALSE) FILTERING PROBES BY FLAGS Error in is(ddNORM, "uRNAList") : object 'ddNORM' not found -- Karthik K.N [[alternative HTML version deleted]]
probe AgiMicroRna probe AgiMicroRna • 909 views
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