Question: [simpleaffy] maizecdf.qcdef
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gravatar for Maciej Jończyk
8.2 years ago by
Maciej Jończyk720 wrote:
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 1
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ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Maciej Jończyk720
Answer: [simpleaffy] maizecdf.qcdef
0
gravatar for Maciej Jończyk
8.2 years ago by
Maciej Jończyk720 wrote:
I've used the file and it seems to work fine. > 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 Best Wishes, Maciej Jonczyk
ADD COMMENTlink written 8.2 years ago by Maciej Jończyk720
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