[BioC] Agi4x44PreProcess: 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)

[Neel Aluru]

Hey Julia,

I think I know what the problem is. I had a similar problem while using the AgiMicroRna package. I think Agilent changed the column heading and Agi4X44PreProcess is not finding Sequence and chr_coord in your input files. The solution for this is you should open your  input files and change the column headings from whatever they say now to Sequence and chr_coord. I know it is a pain but thats the quick fix. Alternatively, you can ask the package maintainer to change that function.

Hope this helps,

Neel

On Jul 28, 2010, at 11:32 AM, Turner, Julia wrote:

> 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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Neel Aluru
Postdoctoral Scholar
Biology Department
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
USA
508-289-3607