[BioC] Kooky probe names (followup)

[Crispin Miller]

Hi,
More information about the probe-names problems I'm having with probe names becoming X12324.at instead of 1234_at


Firstly, this is the version of R I'm using:

>R.version
         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status   Beta
major    1
minor    7.1
year     2003
month    06
day      08
language R


I've managed to reproduce the wierdness with the following minimal script:
I start off with two dataframes:
class(first);
class(second);
> class(first);
[1] "data.frame"
> class(second);
[1] "data.frame"

containing some numbers calculated for each probeset (these are both generated using identical functions, just comparing different groups of chips):

first[1:2,]
second[1:2,]

> first[1:2,]
          X1        X2        X3       X4
1007_s_at  0 0.1218871 0.2664602 1.202853
1053_at    0 0.2757304 0.4460427 1.362298
> second[1:2,]
          X1        X2          X3        X4
1007_s_at  0 0.6255407 -0.08225843 -1.058674
1053_at    0 0.6037322 -0.19470686 -1.144492

I then find entries where X2<0.05 in each data.frame:
> first[first$X2<0.5,][1:2,]
          X1        X2        X3       X4
1007_s_at  0 0.1218871 0.2664602 1.202853
1053_at    0 0.2757304 0.4460427 1.362298
> second[second$X2<0.5,][1:2,]
           X1         X2          X3        X4
X121.at     0 0.09278053 -0.19887301 -1.147801
X1255.g.at  0 0.41586962  0.09071178  1.064895

Weird!

Now, I play a bit:
> second[1:2,][1:2,]
          X1        X2          X3        X4
1007_s_at  0 0.6255407 -0.08225843 -1.058674
1053_at    0 0.6037322 -0.19470686 -1.144492
> second[1:2,][1:3,]
           X1        X2          X3        X4
X1007.s.at  0 0.6255407 -0.08225843 -1.058674
X1053.at    0 0.6037322 -0.19470686 -1.144492
NA         NA        NA          NA        NA
>

Does this give a clue as to what's going on?

Cheers,
Crispin
 
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