[BioC] AgiMicroRna problem

[Paulo Nuin]

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