EBSeqHMMTest error

[Martyna Gajos]

Hi,

I get following message and error when I run the EBSeqHMMTest:

 Conditions are ordered as:
 d0 d1 d2 d3 d4
 Estimating parameters when expected FC = 2
Error in dimnames(x) <- dn :
  length of 'dimnames' [1] not equal to array extent

Here is my code:

data <- read.csv(file=f, header=TRUE, row.names=1,check.names=TRUE)
colData <- read.csv(file=mf, header=FALSE, sep="\t", check.names=FALSE)
IsosGeneNames <- read.csv(file=gf, header=FALSE, sep="\t", check.names=FALSE)
IsoNames <- read.csv(file=tf, header=FALSE, sep="\t", check.names=FALSE)

countData <- as.matrix(data)
colnames(countData) <- NULL

IsoSizes=MedianNorm(countData)
NgList=GetNg(IsoNames$V1, IsosGeneNames$V1)
IsoNgTrun=NgList$IsoformNgTrun

IsoMultiOut=EBSeqHMMTest(countData, NgVector=IsoNgTrun,Conditions=colData$V1, sizeFactors=IsoSizes,UpdateRd=10)

And info about the input:

countData

 num [1:175420, 1:35] 1907.3 0 69.3 111.2 0 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:175420] "ENST00000373020.8" "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4" ...
  ..$ : NULL

IsoNgTrun
 num [1:175420(1d)] 3 3 3 3 3 2 2 3 3 3 ...
 - attr(*, "dimnames")=List of 1
  ..$ : chr [1:175420] "ENST00000373020.8" "ENST00000494424.1" "ENST00000496771.5" "ENST00000612152.4" ...

colData$V1
 Factor w/ 5 levels "d0","d1","d2",..: 1 1 4 3 3 1 4 2 1 3 ...

IsoSizes
 num [1:35] 0.9 0.932 0.975 0.986 0.985 ...

Do you have any idea what my mistake might be?