Hi Henrik
Could you please check is there a similar error on DNAcopy as the error for
sfit?
cbs.all <- CbsModel(ds.all,chromosomes=8);
Loading required package: DNAcopy
Failed with error: 'package 'DNAcopy' is not installed for 'arch=i386''
Error in list(`CbsModel(ds.all, chromosomes = 8)` = <environment>,
`throw("Package not loaded: DNAcopy")` = <environment>, :
Many thanks
yan
-----Original Message-----
From: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson
Sent: 05 December 2010 19:06
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] DNA segmentation error: sfit error
Hi,
thanks for reporting on this issue.
On Sun, Dec 5, 2010 at 10:37 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote:
> Dear all,
>
> I'm doing DNA segmentation on affymetrix 100k SNP data, 50k_hind chip data
> works fine, I'm just trying to do the same on Xba chip, but I got the
> following error:
>
> Failed with error: 'package 'sfit' is not installed for 'arch=i386''
> Error in list(`doCRMAv1("Fockens_2", chipType = "Mapping50K_Xba240",
> chromosomes = 8, verbose = TRUE)` = <environment>, :
>
> Then I tried to install sfit:
> source("http://www.braju.com/R/hbLite.R";);
>>installPackages("http://www.braju.com/R/repos/sfit_0.1.9.zip";);
> trying URL 'http://www.braju.com/R/repos/sfit_0.1.9.zip'
> Content type 'application/zip' length 85895 bytes (83 Kb)
> opened URL
> downloaded 83 Kb
>
> Installing package(s) into 'C:\Users\rmhkyji/R/win-library/2.12'
> (as 'lib' is unspecified)
> package 'sfit' successfully unpacked and MD5 sums checked
>> library("sfit");
> Error: package 'sfit' is not installed for 'arch=i386'
I've checked, and it turned out that the Windows binary of 'sfit' was
incorrectly flagged as an x64-only package. I've uploaded a correct
version. Please try again.
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
should do.
>
> I didn't come across this error for hind chip, is this library not used for
> Hind chip?
To clarify, the 'sfit' package is used for the allele-crosstalk
calibration of *any* SNP chip type. The error has nothing to with the
chip type you are trying to process; the error is that the package
'sfit' cannot be loaded. I suspect that when you processed the
Mapping50K_Hind240 chip type, you had a different R setup, than you
have now, e.g. you installed R v2.12.0 since(?). R v2.12.0 do more
rigorous sanity checks when loading Windows binary package and I guess
R v2.11.0 let it pass unnoticed (which in turn is indeed ok with the
'sfit' package).
/Henrik
>
> Many thanks
>
> yan
[snip]
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