[BioC] simpleaffy qc.stats error on mouse4302 arrays

[Michael]

Hi Dick,
I had the same problem, and also with drosophila arrays. If you take a
look at the code for the function qc.stats, it doesn't include
descriptions for the moe430 chips or drosophila, you can edit the else:


else {
      if (n %in% c("rae230acdf")) {
        rats <- 2^cbind((x["AFFX_Rat_GAPDH_3_at",] -
x["AFFX_Rat_GAPDH_5_at",]),
                        (x["AFFX_Rat_GAPDH_3_at",] -
x["AFFX_Rat_GAPDH_M_at",]),
                        (x["AFFX_Rat_beta-actin_3_at",]  -
x["AFFX_Rat_beta-actin_5_at",]),
                       (x["AFFX_Rat_beta-actin_3_at",]  -
x["AFFX_Rat_beta-actin_5_at",]));
      }

by the way, I think the last line in the function above should probably
be AFFX_Rat_beta-actin_M_at" for rat chip users.

to include your moe430 using the rat chip as a template,


else {
      if (n %in% c("moe4302cdf(or whatever your version is)")) {
        rats <- 2^cbind((x["AFFX-GapdhMur/M32599_3_at",] -
x["AFFX-GapdhMur/M32599_5_at",]),
                        (x["AFFX-GapdhMur/M32599_3_at",] -
x["AFFX-GapdhMur/M32599_M_at",]),
                        (x["AFFX-b-ActinMur/M12481_3_at",]  -
x["AFFX-b-ActinMur/M12481_5_at",]),
                       (x["AFFX-b-ActinMur/M12481_3_at",]  -
x["AFFX-b-ActinMur/M12481_M_at",]));
      }


 just be sure to include the correct descriptions for the controls on
the chip.  Leave the rats object alone, because everything refers to
rats.  Rename the function something like qc2.stats and you should be
able to get it working with your chips.

Best,
mike

Michael McDonald Ph.D.
Duboule Lab
Universite de Geneve
Quai Ernest-Ansermet 30
Geneve 1211
Switzerland
41 22 379 67 79
41 22 379 67 95 fax