Dear Neeraj Kumar, You cannot apply Tquantile normalization to your data, because the Tquantile method is only appropriate for two-colour data whereas your data is single-channel. The only valid methods for single-channel data are "scale","quantile" or "cyclicloess". Best wishes Gordon ------------- original message ------------ [BioC] Vector for Targest in Tquantile Normalization for different groups. neeraj rana neerajrana14 at gmail.com Fri Jul 19 15:35:48 CEST 2013 Dear List, I am doing one microarray analysis. I need to perform Tquantile Normalization for different groups.For that i need to make one vector to define groups. Here is my analysis. y.q <- normalizeBetweenArrays(y, method="Tquantile",targets="*how to make targets vector here??*") > targets <- readTargets("limma_target1.txt") > x <- read.maimages(targets, source="agilent",green.only=TRUE) Read US11093882_251897210520_S01_GE1_107_Sep09_1_2.txt Read US90403632_251897210554_S01_GE1_107_Sep09_1_3.txt Read US11093882_251897210520_S01_GE1_107_Sep09_1_3.txt Read US11093882_251897210520_S01_GE1_107_Sep09_1_4.txt Read US90403632_251897210554_S01_GE1_107_Sep09_1_4.txt Read US11093882_251897210520_S01_GE1_107_Sep09_1_1.txt > targets SampleNumber FileName Condition 1 2 US11093882_251897210520_S01_GE1_107_Sep09_1_2.txt C3 2 3 US90403632_251897210554_S01_GE1_107_Sep09_1_3.txt C3 3 4 US11093882_251897210520_S01_GE1_107_Sep09_1_3.txt C3 4 5 US11093882_251897210520_S01_GE1_107_Sep09_1_4.txt C9 5 6 US90403632_251897210554_S01_GE1_107_Sep09_1_4.txt C9 6 1 US11093882_251897210520_S01_GE1_107_Sep09_1_1.txt C9 y.q <- normalizeBetweenArrays(y, method="Tquantile",targets="*how to make targets vector here*") Thanks . -- Neeraj Kumar ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}