[BioC] problems normalizing in limma

Anand C. Patel acpatel at usa.net
Thu Oct 13 18:38:44 CEST 2005

A quick look at the CSV files generated by PerkinElmer's ScanArray  
finds a bottom row that only has in it "END DATA".  Thus, as Dr.  
Smyth predicted:
 > RG2$R[38977,]
slide_13295067 slide_13295072 slide_13295071 slide_13295073  
slide_13295075 slide_13295079 slide_13295080 slide_13295203  
slide_13295068 slide_13295214
             NA             NA             NA              
NA             NA             NA             NA              
NA             NA             NA
slide_13295879 slide_13295887
             NA             NA
Are we the only people using PerkinElmer's ScanArray software?  I did  
my due diligence in terms of searching the list archives prior to  
posting, and didn't see any other posts.  It is frustrating that even  
the "standard" gpr format would not work, and that the csv format  
output is nonstandard.  However, it doesn't seem like it should be  
terribly difficult to modify the genepix routine in read.maimages  
into a "scanarray_gpr" option, much as was done with bluefuse.  Is  
this something I should work through and submit?  Also, besides the  
obvious step of going through the CSV files and erasing the last row,  
is there an easy way to remove row 38977 from the RGlist as a whole?

Much thanks to Dr. Smyth for both limma and his assistance.

Anand C. Patel, MD
Washington University School of Medicine
acpatel at usa.net

 >[BioC] problems normalizing in limma
 >Gordon Smyth smyth at wehi.edu.au
 >Thu Oct 13 12:25:57 CEST 2005
 >Previous message: [BioC] annotations for Codelink arrays
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 >The output you give shows that all your intensity matrices (R, G,  
Rb and
 >Gb) are one row longer than your annotation data.frame RG2$genes. This
 >cannot be. The layout information agree with the dimension of RG2 
 >My guess is that your input gpr files contained a spurious extra  
row which
 >is not real data. If so, you need to fix them to remove this  
spurious row,
 >or simply remove the last row of all the intensity columns. (Check  
 >that RG2$R[38977,] is not real data.)

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