[BioC] duplicate correlation of 4 "within array replicates" limma gui

Naomi Altman naomi at stat.psu.edu
Thu Oct 9 22:44:03 CEST 2008

The "no-brainer" solution is to presort the 
arrays by mer-label.  That would make the spacing=1.


At 02:07 PM 10/8/2008, Christine Voellenkle wrote:
>Dear all,
>I perform 2 color hybridization, using microRNA and Exiqon slides.
>slide design: 4 replicates of 1 array
>                    each array consits of 8 subarrays,
>                    each subarray of 16 columns and 11 rows
>                    each mir has 4 replicates
>For analysis of the data I use limma GUI, to obtain the p-values of
>differentially expressed mirs I carried out loess normalization
>(backgroundsubstraction normexp, offset=10) and subsequently applied the
>Linear model fit, which works, as long as I treat  each replicate like a
>single mir.
>I would like to now also about the correlation of the replicates, so I
>entered as replicate number 4 and as distance 21 (according to
>"Bioinformatics+ computional statistics using R and Bioconductor" the
>distance corresponds to the number of spots that lies betweeen the
>But I get the following message:
>"Error in dim(M)<- c(spacing,ndups, ngroups, nslides)
>dims[product 5628] do not match the length of object [5632]"
>I rechecked the gal file and recounted on the image, 21 is the correct
>number (considering the column-distance, using the number of spots of row
>distance results in dims[product 0]).
>I read the limma guide and checked also the examples on the limma gui
>homepage, but it's always either no replicate or only 2 replicates next to
>each other.
>Do you know a solution?
>Also another question:
>IF one day I manage to do the duplicate correlation and given that I would
>use weights to identfy features with the flag "bad", how will the software
>handle this if one or more replicates are flagged bad? will it exclude the
>flagged bad replicate from the correlation?
>If yes, is there a way to put a minimum limit of 2 unflagged spots per mir,
>so that in case of only 1 unflagged replicate of a mir to exclude this mir
>from analysis?
>Thank you  a lot in advance!
>Greetings, Christine
>Dr. Christine Völlenkle, Ph.D.
>Research Laboratories-Molecular Cardiology
>I.R.C.C.S. Policlinico San Donato
>Via R. Morandi, 30
>20097  S. Donato M.se (MI) Italy
>Phone: +39 02 52774 683 (lab)
>           +39 02 52774 533 (office)
>Fax:    +39 02 52774 666
>email: christine.voellenkle at gmail.com
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>Bioconductor at stat.math.ethz.ch
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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