limma printer layout
0
0
Entering edit mode
@vanessa-vermeirssen-2253
Last seen 9.6 years ago
Hi, I am trying to read in cDNA spotted microarray data into limma. I would like to check for spatial heterogeneity in the samples and therefore I would like to define the printer layout. I have done this now using a dataframe containing the gene list and columns for block, row and column of the array. Through getLayout, I get correctly the 4 by 8,26 by 26 dimensions (21632 spots). However I noticed from the raw data that in every block at row 26, 4 columns are skipped, so 4 spots are skipped. Therefore in my datafile I only have 21504 spots. When I try to check for spatial heterogeneity by: > imageplot(log2(RG_e1a$Gb[,1]),RG_e1a$printer) Error in imageplot(log2(RG_e1a$Gb[, 1]), RG_e1a$printer) : Number of image spots does not agree with layout dimensions I get this error... Is there a way to more precisely define my printer-layout or a way to get around this and look at spatial heterogeneity anyway? I now copy my code completely, so you have an idea of what I have read in already. #reading cDNA spotted arrays in Limma Bioconductor package library(limma) targets_e1a <- readTargets() RG_e1a <-read.maimages(targets_e1a$FileName, columns=list(R="CH2I_MEDIAN", G="CH1I_MEDIAN",Rb="CH2B_MEDIAN",Gb="CH1B_MEDIAN"), annotation=c("NAME","Orfname","SECTOR","SECTORROW","SECTORCOL")) names(RG_e1a$genes) <- c("ID", "Orfname", "Block", "Row", "Column") RG_e1a$printer <- getLayout(RG_e1a$genes, guessdups=TRUE) Thank you so much already, Vanessa -- ================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 23 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei at psb.ugent.be http://www.psb.ugent.be
Microarray limma Microarray limma • 798 views
ADD COMMENT

Login before adding your answer.

Traffic: 586 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6