[BioC] problem for dealing with replicated spots in slide

[Gordon K Smyth]

The limma package has integrated support for replicated spots.  In the
terminology of that package you have ndups=3 and spacing=1.  See lmFit()
and eBayes().

> Hi,
>
> I'm learning using marray package to analyze microarray data. After
> studying the tutorial  using data 'swirl', I found each spot in this
> tutorial slide stands for one gene.  My data have a little difference.
> These are 3 replicated spots in each slide.  I didn't find the comand
> dealing with replicated spots when I followed the tutorial,  So, when I
> analyzed 4 replicated slides and output the gene list using command
> sunch as "stat.bayesian" function,

stat.bayesian is not actually a bioconductor function but rather a
function from the older SMA package.  It's been superceded by the ebayes
function in limma.  You may need to upgrade your packages.

Gordon

 each gene ID in the list stands for
> only one spot in the slides instead of 3 replicated spots. I want each
> gene stands for all spot data including 3 replicated spots  in each
> slide. Can sombody give me some hints to deal with this case? If I need
> to set up some arguments in marrayLayout or I have to write some
> function?
>
> My data is GenePix fata, My Gal file like this:
>
> ATF     1
> 43    5
> Type=GenePix ArrayList V1.0
> BlockCount=40
> BlockType = 0
> "Block1=    2600    17000    140    16    250    18    250"
> .........
> "Block40=    16100    57500    140    16    250    18    250"
>
> Block    Row    Column    ID    Name
> 1    1    1    QHA10A21.yg.ab1    sf_1_1
> 1    1    2    QHA10A21.yg.ab1    sf_1_1
> 1    1    3    QHA10A21.yg.ab1    sf_1_1
> 1    1    4    QHA10P20.yg.ab1    sf_1_3
> 1    1    5    QHA10P20.yg.ab1    sf_1_3
> 1    1    6    QHA10P20.yg.ab1    sf_1_3
> 1    1    7    QHA11H15.yg.ab1    sf_1_5
> 1    1    8    QHA11H15.yg.ab1    sf_1_5
> 1    1    9    QHA11H15.yg.ab1    sf_1_5
> 1    1    10    QHA11O07.yg.ab1    sf_1_7
> 1    1    11    QHA11O07.yg.ab1    sf_1_7
> 1    1    12    QHA11O07.yg.ab1    sf_1_7
> ...........
>
> Thanks
>
> Yi
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor