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
nene could you please share the command to retrieve genes names along with genes symbol? your help will be really appreciated.