Hi,
super busy with huge backlog so I cannot really start replying to
aroma.affymetrix questions until late next week, but I'll make an
exception for this case.
On Thu, Mar 5, 2009 at 10:41 AM, wukong <wukongsu...@gmail.com> wrote:
>
> Dear aroma.affymetrix group users:
>
> Our server suddenly went down when I was running my script on a large
> number of 500K SNP arrays.
> Actually it has finished the "FragmentLengthNormalization"step, and
> the resulting CEL files were in the directory of "plmData
> \mySample,ACC,-XY,QN,RMA,A+B,FLN,-XY".
>
> In my script, the FL-normalized chip effects were stored in an
> "cesNList" object, and the statements below were
> to export the raw copy numbers.
>
> cbs <- CbsModel(cesNList)
> print(cbs)
>
> for(i in 1:n) {
> for(j in 1:23) {
> rawCNs <- extractRawCopyNumbers(cbs, array=i, chromosome=j)
> rawCNs <- as.data.frame(rawCNs)
> write.table(rawCNs)
> }
> }
>
>
> In this step I encountered a power-down. How can I continue my job
> from the break point without
> do the low-level processing again (time not permitting) ?
This is actually what the package was designed to be robust against.
The easiest is actually to rerun the complete script from start. The
thing is that the results from all intermediate steps are stored on
file, and aroma.affymetrix will automatically detect what steps/arrays
are complete and just skip them; it won't redo the analysis for those.
If you have a really large number of arrays in your data set (how
many?), there might be a noticeable delay in each process()/fit()
step, because the processed output is still loaded and validated,
before moving on to the next step.
Due to the instant failure, you might have a corrupt file in your
output, so you might want to redo that last writing of raw CN data
from scratch.
Let us know if this works.
I leave the other question to someone else or to be answer by me next
week or so.
Cheers,
Henrik
>
> Another question is that "extractRawCopyNumbers" takes array numbers
> (1:n) as the argument, but
> how the array numbers corresponds to the actual CEL file names?
> I guess there must be a object there for the name mapping, but I did
> not find it.
>
>
> Many thanks in advance ! Have a nice weekend!
>
>
> ttt
>
>
>
>
> >
>
--~--~---------~--~----~------------~-------~--~----~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe from this group, send email to
aroma-affymetrix-unsubscr...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
