[BioC] Vector for Targest in Tquantile Normalization for different groups

[Gordon K Smyth]

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

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