[BioC] Loading data into AgiMicroRna

[Stephen Taylor]

Hi,

I am trying to use the AgiMicroRna package on Linux but I get an error when trying to read in the Agilent files of my data.

 >dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) 

Error in readGenericHeader(fullname, columns = columns, sep = sep) :
   Specified column headings not found in file

My targets file looks like

FileName        Treatment       GErep
US45102931_252182712973_S01_miRNA_107_Sep09_1_1_DNA10203-001.txt        CON     1
US45102931_252182712973_S01_miRNA_107_Sep09_1_2_DNA10203-002.txt        CON     1
US45102931_252182712973_S01_miRNA_107_Sep09_1_3_DNA10203-004.txt        C1      2
US45102931_252182712973_S01_miRNA_107_Sep09_1_4_DNA10203-005.txt        C1      2
US45102931_252182712973_S01_miRNA_107_Sep09_2_1_DNA10203-006.txt        C1      2
US45102931_252182712973_S01_miRNA_107_Sep09_2_2_DNA10203-007.txt        C2      3
US45102931_252182712973_S01_miRNA_107_Sep09_2_3_DNA10203-008.txt        C2      3
US45102931_252182712973_S01_miRNA_107_Sep09_2_4_DNA10203-009.txt        C2      3
US45102931_252182712974_S01_miRNA_107_Sep09_1_1_DNA10203-010.txt        C3      4
US45102931_252182712974_S01_miRNA_107_Sep09_1_2_DNA10203-011.txt        C3      4
US45102931_252182712974_S01_miRNA_107_Sep09_1_3_DNA10203-012.txt        C3      4


The column headers for my Agilent files are:


FEATURES        FeatureNum      Row     Col     SubTypeMask     ControlType     ProbeName       SystematicName 
PositionX       PositionY gProcessedSignal        gProcessedSigError      gMedianSignal   gBGMedianSignal gBGPixSDev 
   gIsSaturated    gIsFeatNonUnifOL  gIsBGNonUnifOL  gIsFeatPopnOL   gIsBGPopnOL     IsManualFlag    gBGSubSignal 
gIsPosAndSignif gIsWellAboveBG  SpotExtentX       gBGMeanSignal   gTotalProbeSignal       gTotalProbeError 
gTotalGeneSignal        gTotalGeneError gIsGeneDetected


I notice in the readMicroRnaAFEfunction it is looking for chr_coord, gBGUsedgTotalGeneSignal and 
gTotalProbeSignalgMeanSignal which do not appear in the input files.

Any thoughts how I can get the data to load?

 >sessionInfo() 

R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=en_GB.ISO-8859-1       LC_NUMERIC=C
  [3] LC_TIME=en_GB.ISO-8859-1        LC_COLLATE=en_GB.ISO-8859-1
  [5] LC_MONETARY=C                   LC_MESSAGES=en_GB.ISO-8859-1
  [7] LC_PAPER=en_GB.ISO-8859-1       LC_NAME=C
  [9] LC_ADDRESS=C                    LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.ISO-8859-1 LC_IDENTIFICATION=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_1.26.1
[4] limma_3.4.3           Biobase_2.8.0

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


Kind regards and thanks,

Steve