Hi Steve,

I am copying the mail from Pedro to the mailing list. I am thinking if you can read the files using read.maimages function it should work. 

HTH
Neel


Hi Neel and Richard,
Thanks for your patience.  
 
I have slitghtly modified some code in the package, basically related to the way read.maimages is used. I have eliminated the use of the “chr_coord” column in some of the output files which it was what it was causing problems. Before these changes are made effective in the library, please, try this temporal solution:
 
dd=read.maimages(files=targets$FileName,source="agilent",
             columns=list(Rf="gTotalGeneSignal",
                                                        Gf="gTotalProbeSignal",
                                                        Rb="gMeanSignal",
                                                        Gb="gProcessedSignal"),
                           other.columns=list(IsGeneDetected="gIsGeneDetected",
                                                                       IsSaturated="gIsSaturated",
                                                                       IsFeatNonUnifOF="gIsFeatNonUnifOL",
                                                                       IsFeatPopnOL="gIsFeatPopnOL",
                                                                     probe_mappings="probe_mappings",
                                                                       BGKmd="gBGMedianSignal",
                                                                       BGKus="gBGUsed"),
                             annotation = c( "ControlType", "ProbeName","GeneName"),
                             verbose=TRUE,sep="\t",quote="")
 
 
before doing anything else, please check first  that you have “probe_mappings” in the fifth position of “dd$other”
> names(dd$other)[5]
[1] "probe_mappings"
 
Then, change the name of “probe_mappings” to the name that AgiMicroRna uses for this variable:
> names(dd$other)[5] = "chr_coord"
 
Then, use the rest of the functions as usual:
 
ddTGS.rma = rmaMicroRna(dd, normalize = TRUE, background = FALSE) 
ddPROC = filterMicroRna(ddTGS.rma,
            dd,
            control = TRUE,
            IsGeneDetected = TRUE,
            wellaboveNEG = FALSE,
            limIsGeneDetected = 50,
            limNEG = 25,
            makePLOT = FALSE,
            targets,
            verbose = TRUE)
 
 
Please, let me know if you still have any problem. Thanks
 
p.-



On Oct 11, 2010, at 9:26 AM, Stephen Taylor wrote:

> Hi,
> 
>> 
>> You can find the answer to this in the mailing list archives. Pedro answered this couple of times. Search the archives for AgiMicroRna and you will have the answer.
>> 
> 
> Thanks. The solution seems to be:
> 
> >If the data is extracted with the FE report set to 'Full' rather than 'Compact', then it reports the gMeanSignal and >gBGUsed (but not chr_coord).  You can then follow the package using the amendments Pedro posted to get around not >having the chr_coord column.
> 
> 
> I have got the files via a third party who got the samples processed by a company and I am not sure I will be able to get them to set FE report to "Full". Is there another workaround?
> 
> Thanks,
> 
> Steve
> 
> 
>> Neel
>> 
>> On Oct 11, 2010, at 8:48 AM, Stephen Taylor wrote:
>> 
>>> 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
>>> 
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@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
>> 
>> 
>> 
> 

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




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