Question: mutually add a tab in the beggining of the header to make it a valid RMA format
0
gravatar for Angel
4.4 years ago by
Angel40
Berlin
Angel40 wrote:

Hello friends, please help me

i entered these codes, but whenever i use the output as input to geworkbench, it says that" could not parse line #1, line should have 12 columns but has 13 columns, which need manually add a tab at the beggining of the header to make it a valid RMA format"

 library(affy)

> data <- ReadAffy()
> exp <- rma(data)

Background correcting
Normalizing
Calculating Expression
> control <- grep("AFFX",rownames(exp))
> exp <- exp[-control,]
> e <- exprs(exp)
> e <- apply(e,1,function(x) x-median(x))
> e.scaled <- t(scale(t(e),center=FALSE))
> write.exprs(exp, file="output.txt", sep="\t")

where i did wrong please??

 

probe affy software error rma • 679 views
ADD COMMENTlink written 4.4 years ago by Angel40
1

It is generally considered bad form to post the same question to two different sites without letting folks know you are doing so.  I just answered your question on the biostars site. 

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Sean Davis21k

Hello sa63_tanha!

It appears that your post has been cross-posted to another site: Please see: https://www.biostars.org/p/150455/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 4.4 years ago by Sean Davis21k

sorry Sean, i thought here is more specific to R then i asked my question here too

ADD REPLYlink written 4.4 years ago by Angel40

The question would have been fine here, too, but not both.

ADD REPLYlink written 4.4 years ago by Sean Davis21k
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