[BioC] AgiMicroRna readMicroRnaAFE error

[Christian Ruckert]

I have data from Agilent Human miRNA Microarray Version3 chips which 
were extracted using FeatureExtractor 10.5.1.1. When trying to invoke 
readMicroRnaAFE on these files I get the following error:

dd.micro = readMicroRnaAFE(targets.micro, verbose=TRUE)
Error in readGenericHeader(fullname, columns = columns, sep = sep) :
   Specified column headings not found in file

It seems like column Rb = "gMeanSignal" is missing in my data. Is it ok 
to use gMedianSignal instead?

Furthermore dd$genes = ddaux$genes[, c(4, 5, 6)] makes problems, as 
ddaux$genes has only 5 columns
Row, Col, ControlType, ProbeName, SystematicName


The first lines of one of my input files:

integer	integer	text	text	float	float	float	float	float	float	float 
boolean	boolean	boolean	boolean	boolean	boolean	boolean	float	boolean 
boolean	float	float	float	float	float	float	boolean
SubTypeMask	ControlType	ProbeName	SystematicName	PositionX	PositionY 
gProcessedSignal	gProcessedSigError	gMedianSignal	gBGMedianSignal 
gBGPixSDev	gIsSaturated	gIsLowPMTScaledUp	gIsFeatNonUnifOL 
gIsBGNonUnifOL	gIsFeatPopnOL	gIsBGPopnOL	IsManualFlag	gBGSubSignal 
gIsPosAndSignif	gIsWellAboveBG	SpotExtentX	gBGMeanSignal 
gTotalProbeSignal	gTotalProbeError	gTotalGeneSignal	gTotalGeneError 
gIsGeneDetected
0	1	miRNABrightCorner30	miRNABrightCorner30	413121	211.44 
2.205295e+002	2.228109e+001	305	48	9.292912e+000	0	0	0	0	0	0	0 
220.53	1	1	53.5237	49.2325	112972	11.5848	112972	11.5848	1
66	1	DarkCorner	DarkCorner	438727	212104	4.665936e+000 
3.214336e+000	79	50	9.037640e+000	0	0	0	0	1	0	0	4.66594	1	0	49.1849 
50.1741	2.20202	5.44024	2.20202	5.44024	0


 > sessionInfo()
R version 2.11.0 RC (2010-04-19 r51778)
x86_64-pc-linux-gnu

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] AgiMicroRna_1.2.0     preprocessCore_1.10.0 affy_1.26.0
[4] limma_3.4.0           Biobase_2.8.0

loaded via a namespace (and not attached):
[1] affyio_1.16.0


Thanks for your help,
Christian