[BioC] numbers for sequence and probenames

[Wolfgang Huber]

Hi Hrishikesh,

> Why don't the numbers from
> summary(hgu95av2probe):199084
> and length(pbn): 201800 don't match?!!
> There are more sequences than probe names?!

199084 is less than 201800 hence there are fewer sequences than probe 
names. The data file from Affymetrix from which the hgu95av2probe table 
was obtained (1:1 without any additions/omissions) contains that number 
of probes. The remainder may be control or 'empty' probes.

   Hope this helps,
    Wolfgang

> 
> I am including code snippet.
> 
> Thanks,
> Hrishi
> 
> data(hgu95av2probe)
> 
>>summary(hgu95av2probe)
> 
>    sequence               x               y        
> Probe.Set.Name    
>  Length:199084      Min.   :  1.0   Min.   :  1.0  
> Length:199084     
>  Class :AsIs        1st Qu.:161.0   1st Qu.:161.0  
> Class :AsIs       
>  Mode  :character   Median :319.0   Median :319.0  
> Mode  :character  
>                     Mean   :319.1   Mean   :319.8     
>                
>                     3rd Qu.:478.0   3rd Qu.:479.0     
>                
>                     Max.   :638.0   Max.   :637.0     
>                
>  Probe.Interrogation.Position Target.Strandedness
>  Min.   :   14                Antisense:198784   
>  1st Qu.:  865                Sense    :   300   
>  Median : 1649                                   
>  Mean   : 2132                                   
>  3rd Qu.: 2856                                   
>  Max.   :20813                                   
> 
> 
>>pbn<-probeNames(M[,1])
>>length(pbn)
> 
> [1] 201800
> 
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-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber