[BioC] [simpleaffy] maizecdf.qcdef

[mjonczyk at biol.uw.edu.pl]

Dear List Members,

I've found that qcdef file for maize isn't available in simpleaffy package.
So I prepared it by myself.

Here it is:

array maizecdf
alpha1 0.05
alpha2 0.065
spk bioB AFFX-r2-Ec-bioB-3_at
spk bioC AFFX-r2-Ec-bioC-3_at
spk bioD AFFX-r2-Ec-bioD-3_at
spk creX AFFX-r2-P1-cre-3_at
ratio actin3/actin5 AFFX-Zm-actin-3_a_at AFFX-Zm-actin-5_a_at
ratio actin3/actinM AFFX-Zm-actin-3_a_at AFFX-Zm-actin-M_a_at
ratio gapdh3/gapdh5 AFFX-Zm-gapdh-3_at AFFX-Zm-gapdh-5_at
ratio gapdh3/gapdhM AFFX-Zm-gapdh-3_at AFFX-Zm-gapdh-M_at

I've constructed it based on simpleaffy manual chapter 5.4 and
qcdef files for Arabidopsis and Poplar.

Maybe someone will find it useful.
If something is wrong with it, please, correct me.

*impotrant* I'm not sure which one gapdh use, in file with controls I have:

>control:maize:*AFFX-Zm-gapdh-3_at*; gb|U45857.1; /DEF=Zea mays
glyceraldehyde-3-phosphate dehydrogenase GAPC4 (gpc4) mRNA, complete cds. 
/GEN=gpc4 /PROD=cytosolic glyceroldehyde-3-phosphatedehydrogenase GAPC4
>control:maize:*AFFX-Zm-gapdh-5_at*; gb|U45857.1; /DEF=Zea mays
glyceraldehyde-3-phosphate dehydrogenase GAPC4 (gpc4) mRNA, complete cds. 
/GEN=gpc4 /PROD=cytosolic glyceroldehyde-3-phosphatedehydrogenase GAPC4
>control:maize:*AFFX-Zm-gapdh-M_at*; gb|U45857.1; /DEF=Zea mays
glyceraldehyde-3-phosphate dehydrogenase GAPC4 (gpc4) mRNA, complete cds. 
/GEN=gpc4 /PROD=cytosolic glyceroldehyde-3-phosphatedehydrogenase GAPC4
>control:maize:*AFFX-Zm-gapdh-M_s_at*; gb|U45857.1; /DEF=Zea mays
glyceraldehyde-3-phosphate dehydrogenase GAPC4 (gpc4) mRNA, complete cds. 
/GEN=gpc4 /PROD=cytosolic glyceroldehyde-3-phosphatedehydrogenase GAPC4

Similarly for actin, in control file there is:
>control:maize:AFFX-Zm-actin-5_at; gb|BG842899; /DB_XREF=MEST41-D02.T3
/CLONE=MEST41-D02
>control:maize:AFFX-Zm-actin-5_x_at; gb|BG842899; /DB_XREF=MEST41-D02.T3
/CLONE=MEST41-D02
>control:maize:AFFX-Zm-actin-5_a_at; gb|BG842899; /DB_XREF=MEST41-D02.T3
/CLONE=MEST41-D02
>control:maize:AFFX-Zm-actin-M_x_at; gb|BG842899; /DB_XREF=MEST41-D02.T3
/CLONE=MEST41-D02
>control:maize:AFFX-Zm-actin-M_a_at; gb|BG842899; /DB_XREF=MEST41-D02.T3
/CLONE=MEST41-D02
>control:maize:AFFX-Zm-actin-3_a_at; gb|BG842899; /DB_XREF=MEST41-D02.T3
/CLONE=MEST41-D02

I've just use values which makes sense for me.

Best Wishes,
Maciej Jonczyk MSc

Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa
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