[BioC] NormalizeBetweenArrays

[Gordon Smyth]

Dear Jason,

At 04:35 AM 11/03/2004, Jason Skelton wrote:
>Hi  Gordon and everyone
>
>i'm using (Limma V1.5.1, R V1.8.0)
>
>I have an experiment with seven treatments as outlined below
>
>   Germball Cerc TwoDay SevenDay TwentyOneDay AdultWorm Egg
>1        -1    0      0        0            0         0   0
>2        -1    0      0        0            0         0   0
>3        -1    0      0        0            0         0   0
>4         1    0      0        0            0         0   0
>5         0   -1      0        0            0         0   0
>6         0   -1      0        0            0         0   0
>7         0   -1      0        0            0         0   0
>8         0    1      0        0            0         0   0
>9         0    0     -1        0            0         0   0
>10        0    0     -1        0            0         0   0
>11        0    0     -1        0            0         0   0
>12        0    0      1        0            0         0   0
>13        0    0      0        1            0         0   0
>14        0    0      0       -1            0         0   0
>15        0    0      0       -1            0         0   0
>16        0    0      0       -1            0         0   0
>17        0    0      0        0           -1         0   0
>18        0    0      0        0           -1         0   0
>19        0    0      0        0           -1         0   0
>20        0    0      0        0            1         0   0
>21        0    0      0        0            0         1   0
>22        0    0      0        0            0        -1   0
>23        0    0      0        0            0        -1   0
>24        0    0      0        0            0        -1   0
>25        0    0      0        0            0         0  -1
>26        0    0      0        0            0         0  -1
>
>I'm currently using normalizeWithinArrays for each of the 26 slides and 
>treating them completely seperately
>then liner model fitting ->  classifyTests etc................
>
>However I'd like to normalize within treatments
>
>Is there an easy way of taking the normalized *within* arrays results
>and *normalizing between arrays* for each treatment seperately then 
>combining these back in to a complete MAlist ?

This isn't built-in to limma but it is easy to do using the subset and 
cbind operations defined for MAList objects. Suppose that 'design' is the 
matrix you give above and 'MA' is your within-array normalized data object.

MA1 <- MA[, as.logical(design[,"Germball"])]
MA1 <- normalizeBetweenArrays(MA1, method="Aq")

MA2 <- MA[, as.logical(design[,"Cerc"])]
MA2 <- normalizeBetweenArrays(MA1, method="Aq")

etc, then

MAnorm <- cbind(MA1,MA2,MA3,MA4,MA5,MA6,MA7)

Gordon

>for use in further downstream analysis to compare treatments using 
>ClassifyTests etc ?
>
>Many thanks
>
>J.
>
>
>
>--
>--------------------------------
>Jason Skelton
>Pathogen Microarrays
>Wellcome Trust Sanger Institute
>Hinxton
>Cambridge
>CB10 1SA
>
>Tel +44(0)1223 834244 Ext 7123
>Fax +44(0)1223 494919