[BioC] help regarding tutorial Lab5 and Lab6

[Claire Wilson]

Hi dibaker,

I can answer part of your question (I think!)

> # DO NOT UNDERSTAND THE FOLLOWING LINES.
> 
>  > golubTrainSub <- golubTrain[sub, ]

select only the rows of golubTrain that appear in sub

>  > golubTrainSub at exprs <- X

set the expression value slot of the golubTrainSub expression set to the values contained in X

>  > Y <- golubTrainSub$ALL.AML

Make Y the same as the ALL>AML column in golubTrainSub

> 
> #I UNDERSTAND THE FOLLOWING LINE
>  > Y <- paste(golubTrain$ALL.AML, golubTrain$T.B.cell)
> 
> # DO NOT UNDERSTAND THE FOLLOWING ONE.
>  > Y <- sub("NA", "", Y)

In this instance I beleive you are substituting all NA's in Y for "" (do ?sub at the R command line)

> ---------- Problem no 2 ----------------------
>  From Lab6 Code, the following is OK
> ================================
>  > data(golubTrain)
>  > data(golubMerge)
>  > data(golubTest)
>  > gTrn <- GolubTrans(golubTrain)
>  > gTest <- GolubTrans(golubTest)
>  > gMerge <- GolubTrans(golubMerge)
>  > mmfun <- mmfilt()
>  > ffun <- filterfun(mmfun)
>  > sub <- genefilter(gTrn, ffun)
> 
> But why we need to set the following element False?
> 
>  > sub[c(2401, 3398, 4168)] <- FALSE

Can't help here I am afraid!


Hope the above helps

claire
--
Claire Wilson, PhD   
Bioinformatics group  
Paterson Institute for Cancer Research  
Christies Hospital NHS Trust  
Wilmslow Road,  
Withington  
Manchester  
M20 4BX  
tel: +44 (0)161 446 8218  
url: http://bioinf.picr.man.ac.uk/
 
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