[R] analyse tab delimited textfile microarray data(help)

[Martin Morgan]

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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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