Dear all,

I import a txt file into an arrayCGH object:

 

> arrayAB <- import("arAB.txt", type="default", spot.names=spot.names,
clone.names=clone.names,

design=c(8,4,26,26), add.line=T, id.rep=1)

 

> nrow(arrayAB$arrayValues)

[1] 21632

 

> nrow(arrayAB$cloneValues)

[1] 3588

 

And then I normalized the object by using the MANOR package: 

 

> arrayAB.norm <- norm.arrayCGH(arrayAB, var="LogRatio", FUN=median,
na.rm=TRUE)

 

I have two questions: 

1.	what’s na.rm? 
2.	where can I found the “single target value computed for all the
replicates”? Is it arrayAB.norm$cloneValues$LogRatio?

 

> names(arrayAB.norm$cloneValues)

[1] "ID"       "Chr"      "Position" "LogRatio" "rep"      "rep0"
"FlagAgr" 

[8] "FlagT"   

 

Thanks a lot!

Michela

 

 

 

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Michela Ballardini

Unità di Biostatistica e Sperimentazioni Cliniche - Pad. Valsalva

c/o OSP. MORGAGNI-PIERANTONI

Via Forlanini, 34

47100 Forlì

Tel. (+39) 0543.731836

Fax (+39) 0543.731612

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