Hello, i am trying to analyse Agilent array which doesn't have gMeansignal(instead it has gBGMeansignal).Although by replacing gMeansignal with gBGmeansignal i am able to read the file but it is showing error "Error in xy.coords(x, y) : 'x' and 'y' lengths differ" in tgsNormalization step.Kindly tell me the solution? This array works fine when using limma alone.
> setwd("F:/R/microarray/agimirna/scan2")
> library("AgiMicroRna")
> library("limma")
> mytargets.micro=readTargets("scan2.txt")
> print(mytargets.micro)
FileName Treatment GErep Subject
FC_1.2 FC_1.2.txt A 1 1
FC_2.2 FC_2.2.txt A 1 1
FC_3 FC_3.txt A 1 1
FS_1.2 FS_1.2.txt B 2 1
FS_2.2 FS_2.2.txt B 2 1
FS_3 FS_3.txt B 2 1
IRC_1.2 IRC_1.2.txt C 3 1
IRC_2.2 IRC_2.2.txt C 3 1
IRC_3 IRC_3.txt C 3 1
IRS_1.2 IRS_1.2.txt D 4 1
IRS_2.2 IRS_2.2.txt D 4 1
IRS_3 IRS_3.txt D 4 1
NRC_1.2 NRC_1.2.txt E 5 1
NRC_2.2 NRC_2.2.txt E 5 1
NRC_3 NRC_3.txt E 5 1
NRS_1.2 NRS_1.2.txt F 6 1
NRS_2.2 NRS_2.2.txt F 6 1
NRS_3 NRS_3.txt F 6 1
SC_1.2 SC_1.2.txt G 7 1
SC_2 SC_2.txt G 7 1
SC_3 SC_3.txt G 7 1
SS_1.2 SS_1.2.txt H 8 1
SS_2.2 SS_2.2.txt H 8 1
SS_3.2 SS_3.2.txt H 8 1
> mydd.micro=AgiMicroRna:::read.agiMicroRna(mytargets.micro,
+ columns=list(TGS="gTotalGeneSignal",
+ TPS="gTotalProbeSignal",
+ meanS="gBGMeanSignal",
+ procS="gProcessedSignal"),
+ other.columns=list(IsGeneDetected="gIsGeneDetected",
+ IsSaturated="gIsSaturated",
+ IsFeatNonUnifOF="gIsFeatNonUnifOL",
+ IsFeatPopnOL="gIsFeatPopnOL",
+ BGKmd="gBGMedianSignal",
+ BGKus="gBGUsed"),
+ annotation = c( "ControlType", "ProbeName","GeneName"),
+ verbose=TRUE)
reading file 1 - FC_1.2.txt
reading file 2 - FC_2.2.txt
reading file 3 - FC_3.txt
reading file 4 - FS_1.2.txt
reading file 5 - FS_2.2.txt
reading file 6 - FS_3.txt
reading file 7 - IRC_1.2.txt
reading file 8 - IRC_2.2.txt
reading file 9 - IRC_3.txt
reading file 10 - IRS_1.2.txt
reading file 11 - IRS_2.2.txt
reading file 12 - IRS_3.txt
reading file 13 - NRC_1.2.txt
reading file 14 - NRC_2.2.txt
reading file 15 - NRC_3.txt
reading file 16 - NRS_1.2.txt
reading file 17 - NRS_2.2.txt
reading file 18 - NRS_3.txt
reading file 19 - SC_1.2.txt
reading file 20 - SC_2.txt
reading file 21 - SC_3.txt
reading file 22 - SS_1.2.txt
reading file 23 - SS_2.2.txt
reading file 24 - SS_3.2.txt
> class(mydd.micro)
[1] "uRNAList"
attr(,"package")
[1] "AgiMicroRna"
> dim(mydd.micro)
[1] 15744 24
> print(names(mydd.micro))
[1] "TGS" "TPS" "meanS" "procS" "targets" "genes"
[7] "other"
> myddTGS=tgsMicroRna(mydd.micro,
+ offset=5,
+ half=FALSE,
+ makePLOT=FALSE,
+ verbose=FALSE)
Warning message:
In min(ddTGS$TGS) : no non-missing arguments to min; returning Inf
> myddNORM=tgsNormalization(myddTGS,
+ "quantile",
+ makePLOTpre=FALSE,
+ makePLOTpost=FALSE,
+ mytargets.micro,
+ verbose=TRUE)
Error in xy.coords(x, y) : 'x' and 'y' lengths differ
> ddTGS.rma=rmaMicroRna(mydd.micro,normalize=TRUE,background=TRUE)
Error in split.default(0:(length(pNList) - 1), pNList) :
group length is 0 but data length > 0
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