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 NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. [[alternative HTML version deleted]]

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 > > > > > > NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > Neel Aluru Postdoctoral Scholar Biology Department Woods Hole Oceanographic Institution Woods Hole, MA 02543 USA 508-289-3607