Dear all,

This is my first post asking for help in R. I have read your posts and I have applied them successfully in all my analysis. I am analyzing a set of Affymetrix Mouse Gene 2.0 ST arrays. I have used the oligo package to process the data, the limma for the statistical analysis and the following command to get the annotations:

fit2$genes$Symbol<-unlist(mget(fit2$genes$ID, mogene20sttranscriptclusterSYMBOL, ifnotfound=NA))

Until this point all was OK, and I have check in the Affymetrix website that the annotations are correct. However, I found a problem when I removed the Affy control probesets or when I filtered by standard deviation of the probesets (using nsFilter). Once I filtered, I used limma again but when I tried to annotate again, the result was wrong:

These are the annotations before (I checked them in the Affymetrix website):

                     Symbol      logFC             AveExpr              t
17335467       Cdkn1a  -2.323171754   7.223331238    -10.37320661
17212087       Npas2   -2.081290451   6.59909809     -8.235582159
17335297       Ppard   -1.32763864    7.595112276    -7.040890392
17423792       Pnrc1   -1.082579689   7.636240116    -7.887408967
17328625       Sdf2l1  -0.88410546    9.184660965    -7.727213134
17421550       Mthfr   -0.981370712   7.118936687    -7.55630387

And these, after removing the Affymetrix controls (they are wrong):

                      Symbol     logFC            AveExpr                 t
17335467       Cnga3   -2.323171754   7.223331238    -12.97042613
17212087       NA      -2.081290451   6.59909809     -11.54111132
17335297       D430040 -1.32763864    7.595112276    -7.467038424
17423792       Dhrs7b  -1.082579689   7.636240116    -6.141088323
17328625       NA      -0.88410546    9.184660965    -5.030167717
17421550       NA      -0.981370712   7.118936687    -5.572641626

Could anyone help or explain me what is happening?

Thank you so much!

Alberto Valdés