AgiMicroRna_Error in xy.coords(x, y) : 'x' and 'y' lengths differ(tgsNormalization)
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cpsingh9 • 0
@cpsingh9-11481
Last seen 6.2 years ago

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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AgimicroRNA • 815 views
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