Hi all,

 

I want to do a combined analysis looking at single channels of mostly double
channel arrays.  However for 3 of the arrays, only one group of cDNA was
hybridized and therefore they were scanned with one wavelength.

 

I was getting Error Message #1 as below:  Reading through old BioC help
emails, I noticed a few people having problems if the number of header lines
was different.  So I changed this by adding 5 line corresponding to
Normalization factors (making these all equal to 1 for the single channel
arrays).

 Now I get error Message #2.  Has anyone seen this before, or have any
advice about combined analyses for single and double channel arrays.

 

Thanks,

 

alison

 

Error Message #1

> library(limma)

> targets<-readTargets("chlorTargets.txt")

> RG<-read.maimages(targets$FileName,source="genepix")

Read july11_2812.gpr 

Read july11_7261.gpr 

Read july11_7322.gpr 

Read july11_0740.gpr 

Read 797scan2bckp.gpr 

Read 729Sscan2.gpr 

Read 723scan1.gpr 

Error in readGPRHeader(fullname) : File is not in Axon Text File (ATF)
format

In addition: Warning message:

incomplete final line found by readLines on '716scan1.gpr' 

> 

 

Error Message #2.

 

Error in "[.data.frame"(obj, , columns[[a]]) : 

        undefined columns selected

 

******************************************
Alison S. Waller  M.A.Sc.
Doctoral Candidate
awaller@chem-eng.utoronto.ca
416-978-4222 (lab)
Department of Chemical Engineering
Wallberg Building
200 College st.
Toronto, ON
M5S 3E5

  

 


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