pairwise comparison in R

Question

[onemore100iq]

Hi, I am trying to do

pair<-pairwise.comparison(data.mas5,
                          "celline",
                          c("c.oh","5AzadC.48h"), 
                          data.raw)

but it gave me this error

Error in pms[, x] : subscript out of bounds

This is the covdesc I am using, it is tablimited with no header for the first column

     celline  dose  time
GSM230899.CEL.gz    Melanocytes c 0h
GSM230901.CEL.gz    MelJuSo c 0h
GSM230903.CEL.gz    UACC903 c 0h
GSM230905.CEL.gz    C8161 c 0h
GSM230907.CEL.gz    Neo6 c 0h
GSM230909.CEL.gz    WM1205 c 0h
GSM230911.CEL.gz    WM35 c 0h
GSM230900.CEL.gz    Melanocytes 5AzadC 48h 
GSM230902.CEL.gz    MelJuSo 5AzadC 48h 
GSM230904.CEL.gz    UACC903 5AzadC 48h 
GSM230906.CEL.gz    C8161 5AzadC 48h
GSM230908.CEL.gz    Neo6 5AzadC 48h
GSM230910.CEL.gz    WM1205 5AzadC 48h
GSM230912.CEL.gz    WM35 5AzadC 48h

and this is the 2 lines before pairwise comparison

dfr <-data.frame("c.oh"=c("Melanocytes","MelJuSo","UACC903","C8161","Neo6","WM1205","WM35"),
                 "5AzadC.48h"=c("Melanocytes","MelJuSo","UACC903","C8161","Neo6","WM1205","WM35")) 

expgroups=data.frame("c.oh","5AzadC.48h")

and its class is data.frame

I tried to solve it for days but did not know how would you please help me to figure out why this error and how to fix it Thanks

[onemore100iq]

Any help, I been stuck in for too long, please any help.

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

I've also edited your title. Including "bioinformatics" is not necessary since everything here should be bioinformatics.

Take a look at the help message and examples of pairwise.comparison using ?pairwise.comparison. That might give you a clue what's wrong.

[Matteo Schiavinato]

Can you post the line where you declare pms?

[cpad0112]

@OP: There was a similar post by you and you didn't resolve this: C: Bioinformatics and pairwise.comparison and i am not sure if you need raw data in pairwise comparison. Run without raw data.

pair<-pairwise.comparison(data.mas5, "celline", c("c.oh","5AzadC.48h"))

Example code that works is:

> library(simpleaffy)
> library(affydata)
> data(Dilution)
> eset=mas5(Dilution)
> pairwise.comparison(eset,"liver", c("10","20"))
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 12625 features, 4 samples 
  element names: exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: 20A 20B 10A 10B
  varLabels: liver sn19 scanner
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu95av2

[onemore100iq]

Thanks all. But once i read the covdesc differentally as follow: covdesc <- read.csv("covdesc.txt", sep="\t", header=T, stringsAsFactors = F) it worked from there to the end. Thanks again