right choice? executable problems

[Troels]

Dear Bimbam'ers,
I am investigating a possible relationship between 6 exonic SNPs in
one gene and clearance (quantitative trait) of a drug in 93 patients.
log transformed clearance seem to be normal distributed. I have used
PHASE and thus inferred the individual haplotypes (diplotypes) of the
patients.

1) Is Bimbam a reasonable choice for this analysis? (It seems to me
that it is - but I am new to this type of analysis, and havent been
able to find more than one paper using Bimbam to compare with (I guess
it is still quite new).

2) I downloaded the "executables" onto both a remote access linux
system and to "linux Debian in a window" on my winPC, but in both
cases the files "bimbam_lin" "bimbam_linux_32b" and "bimbam_linux_64b"
didnt work (the systems refers to them as bin files? and not
executables). I tried the windows executable but got too frustrated
because of different commands and keyboard.

hope you can help,

best regards,
Troels
phd student@university of southern denmark

[Matthew Stephens]

On Fri, May 15, 2009 at 8:35 AM, Troels <troels....@gmail.com> wrote:
>
> Dear Bimbam'ers,
> I am investigating a possible relationship between 6 exonic SNPs in
> one gene and clearance (quantitative trait) of a drug in 93 patients.
> log transformed clearance seem to be normal distributed. I have used
> PHASE and thus inferred the individual haplotypes (diplotypes) of the
> patients.
>
> 1) Is Bimbam a reasonable choice for this analysis? (It seems to me
> that it is - but I am new to this type of analysis, and havent been
> able to find more than one paper using Bimbam to compare with (I guess
> it is still quite new).

yes, it seems like just the kind of data it could be applied to. You
could just analyse
the 6 typed SNPs using BIMBAM. You could also use imputation to improve power
(eg using HapMap data on the gene as the "panel", or sequence data if
it is available).

>
> 2) I downloaded the "executables" onto both a remote access linux
> system and to "linux Debian in a window" on my winPC, but in both
> cases the files "bimbam_lin" "bimbam_linux_32b" and "bimbam_linux_64b"
> didnt work (the systems refers to them as bin files? and not
> executables). I tried the windows executable but got too frustrated
> because of different commands and keyboard.
>

Perhaps Grant can give you some help here - I'm not sure what the problem is.
Perhaps you need to change the access options to make them executable?

Matthew

[Troels]

Thank you both for the input!

The " chmod 755 bimbam_* " command worked, making the file executable.

best regards,
Troels

On 16 Maj, 15:52, Matthew Stephens <stephens...@gmail.com> wrote: