Hello,



I am getting and input error when I try to use the Agi4X44PreProcess.  I am using the scanner G2505B.  I made sure to extract these as Full (version 10.7.1.1), but it seems not to have the correct columns. I get the error:

INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = FALSE) :the script will stop now

I would greatly appreciate your advice to remedy this error.



Thanks,

Julia



Example File Feature header (PBB__251485059414_S01-2_GE1_107_Sep09_1_2.txt)

FEATURES        FeatureNum      Row     Col     accessions      chr_coord       SubTypeMask     SubTypeName     StartSequence ProbeUID        ControlType     ProbeName       GeneName        SystematicName  Description     PositionX    PositionY        gSurrogateUsed  gIsFound        gProcessedSignal        gProcessedSigError      gNumPixOLHi     gNumPixOLLo   gNumPix gMeanSignal     gMedianSignal   gPixSDev        gPixNormIQR     gBGNumPix       gBGMeanSignal   gBGMedianSignal       gBGPixSDev      gBGPixNormIQR   gNumSatPix      gIsSaturated    gIsLowPMTScaledUp       gIsFeatNonUnifOL      gIsBGNonUnifOL  gIsFeatPopnOL   gIsBGPopnOL     IsManualFlag    gBGSubSignal    gBGSubSigError  gIsPosAndSignif       gPValFeatEqBG   gNumBGUsed      gIsWellAboveBG  gBGUsed gBGSDUsed       ErrorModel      gSpatialDetrendIsInFilteredSet        gSpatialDetrendSurfaceValue     SpotExtentX     SpotExtentY     gNetSignal      gMultDetrendSignal   gProcessedBackground     gProcessedBkngError     IsUsedBGAdjust  gInterpolatedNegCtrlSub gIsInNegCtrlRange       gIsUsedInMD

R input:

library(Agi4x44PreProcess)

> library(hgug4112a.db) #change if you are using human

 Loading required package: org.Hs.eg.db Loading required package: DBI

> setwd("/home/turnerj/Leah_Test/")

> source("AGI4x44PreProcess.param.txt")

> targets=read.targets(infile=infile)

Target File



FileName

PBB__251485059414_S01-2_GE1_107_Sep09_1_1

PBB__251485059414_S01-2_GE1_107_Sep09_1_1.txt

PBB__251485059414_S01-2_GE1_107_Sep09_1_2 PBB__251485059414_S01-2_GE1_107_Sep09_1_2.txt

                                         Treatment GErep Subject Array

PBB__251485059414_S01-2_GE1_107_Sep09_1_1       6hr     2       A 36264

PBB__251485059414_S01-2_GE1_107_Sep09_1_2    saline     1       A 36608



> dd=read.AgilentFE(targets,makePLOT=FALSE)

Read PBB__251485059414_S01-2_GE1_107_Sep09_1_1.txt

Read PBB__251485059414_S01-2_GE1_107_Sep09_1_2.txt

INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA

USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = FALSE) :

the script will stop now

Here is my session info:

 R version 2.11.1 (2010-05-31)

 x86_64-unknown-linux-gnu

 locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C



 attached base packages:

 [1] stats     graphics  grDevices utils     datasets  methods   base



 other attached packages:

 [1] hgug4112a.db_2.4.1      org.Hs.eg.db_2.4.1      RSQLite_0.9-1

 [4] DBI_0.2-5               Agi4x44PreProcess_1.8.0 genefilter_1.30.0

 [7] annotate_1.26.1         AnnotationDbi_1.10.2    limma_3.4.4

 [10] Biobase_2.8.0



 loaded via a namespace (and not attached):

 [1] splines_2.11.1  survival_2.35-8 xtable_1.5-6





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