R help - Nov 2009 - analyse tab delimited textfile microarray data(help)

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Kumar -- ask on the Bioconductor mailing list

   http://bioconductor.org/docs/mailList.html

see basic workflows at

  http://bioconductor.org/docs/workflows/oligoarrays/

You cannot analyze the data without understanding its source or
questions you are asking, so determine where this data is coming from
and what you are expected to do with it before posting.

Martin

kumar kk wrote:
> Hello
> I have microarray data in tab delimited text file.The main headers and some
> fields are as:
> following are the header:
> 
> FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName
> SystematicName PositionX PositionY LogRatio LogRatioError
> PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError
> rProcessedSigError gMedianSignal rMedianSignal gBGMedianSignal
> rBGMedianSignal gBGPixSDev rBGPixSDev gIsSaturated rIsSaturated
> gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL
> gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag
> gBGSubSignal rBGSubSignal gIsPosAndSignif rIsPosAndSignif
> gIsWellAboveBG rIsWellAboveBG SpotExtentX gBGMeanSignal rBGMeanSignal
> 
> 
> 
> following is the data corresponding to the above header :
> 
> 
> DATA 1 1 1 66 1 DarkCorner DarkCorner 379.607 199.729 -5.98E-01
> 1.10E+00 5.86E-01 2.46E+00 6.21E-01 3.02E+00 1.51E+00 0 0 241 273
> 1.35E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 16.0892 -4.46689 1 0 0 0 65
> 135.479 148.517
> DATA 2 1 2 66 1 DarkCorner DarkCorner 405 199.545 -4.71E-01 1.27E+00
> 7.11E-01 1.83E+00 6.20E-01 2.88E+00 1.55E+00 135 145.5 238 266
> 1.31E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 12.0031 2.05821 1 0 0 0 65
> 131.295 147.49
> DATA 3 1 3 66 1 DarkCorner DarkCorner 430.5 199.5 -2.62E-01 1.55E+00
> 8.66E-01 1.13E+00 6.18E-01 2.66E+00 1.45E+00 128 142.5 237.5 270.5
> 1.30E+02 1.47E+02 0 0 0 0 0 0 0 0 0 0 0 7.41805 -0.318846 1 0 0 0
> 64.8204 130.996 148.231
> DATA 4 1 4 0 0 GT_MTB_142632 chr1:2567359-2567418 455.648 199.519
> 1.89E-03 6.14E-02 9.75E-01 1.18E+03 1.18E+03 1.18E+02 1.18E+02 7776
> 15813 231.5 266 1.29E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 7741.9 15324.2
> 1 1 1 1 57.5363 129.226 148.004
> 
> 
> 
> 
> Please tell me how can we analyse this tab delimited text file of
microarray
> data.
> Please tell me the procedure of analysis.
> 
> thanks
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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