Good. /Henrik
On Thu, Oct 30, 2008 at 8:51 PM, biobee <[EMAIL PROTECTED]> wrote:
>
> thanks, I realised I missed a detail.
>
> Now he workflow runs perfectly.
>
>
>
> On Oct 30, 6:32 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
>> Hi,
>>
>> if you look carefully at the following code:
>>
>>
thanks, I realised I missed a detail.
Now he workflow runs perfectly.
On Oct 30, 6:32 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> if you look carefully at the following code:
>
> for(chiptype in names(csRawList)) {
> cs <- csRawList[[chipType]]
> [...]
> csAccList[[chipTy
Hi,
if you look carefully at the following code:
for(chiptype in names(csRawList)) {
cs <- csRawList[[chipType]]
[...]
csAccList[[chipType]]<- csAcc
}
you'll see that the for loop is using iterator variable 'chiptype'
whereas you get and assign the elements in the lists using 'chipType'.
On Thu, Oct 30, 2008 at 10:59 AM, biobee <[EMAIL PROTECTED]> wrote:
>
> Hi Henrik,
>
> From the csAccList itself the 2nd chiptype doesnot come along.
Then it is pretty clear that something goes wrong when you do the ACC step;
csAccList <- list();
for(chiptype in names (csRawList)){
cs <- csRaw
Hi Henrik,
>From the csAccList itself the 2nd chiptype doesnot come along.
On Oct 30, 1:12 pm, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi,
>
>
>
>
>
> On Wed, Oct 29, 2008 at 9:54 PM, biobee <[EMAIL PROTECTED]> wrote:
>
> > Hi Henrik,
>
> > I ran the script as explained in the 'Paired
Hi,
On Wed, Oct 29, 2008 at 9:54 PM, biobee <[EMAIL PROTECTED]> wrote:
>
> Hi Henrik,
>
> I ran the script as explained in the 'Paired total copy number
> analysis' . The script runs fine all the way,however, I wasnot able to
> get raw CN estimates for both chiptypes. When I print cesFlnList, I
>
Hi Henrik,
I ran the script as explained in the 'Paired total copy number
analysis' . The script runs fine all the way,however, I wasnot able to
get raw CN estimates for both chiptypes. When I print cesFlnList, I
get result for only one of the chiptype.
> cesFlnList
$Mapping50K_Xba240
CnChipEffe
Hi,
the mistake you are doing is that you tell R/aroma.affymetrix to
process both chip types, but you only have/load data for one of them.
You do:
chipTypes <- c("Mapping50K_Hind240", "Mapping50K_Xba240")
and this is what is used in the for loops. If you only want to
process one of the chip ty
Hi Henrik,
I checked and my csAccList[[chipType]] returns NULL. However chipTypes
is not empty. It reurns the following:
> chipTypes
[1] "Mapping50K_Hind240" "Mapping50K_Xba240"
Also my csAccList gives the following output:
> csAccList
$Mapping50K_Hind240
AffymetrixCelSet:
Name: katia-TumorNorma
[I took the freedom to bring this thread back to the mailing list, cf
FAQ. 2008-03-26]
Hi.
On Wed, Oct 22, 2008 at 7:17 AM, biobee wrote:
> Hi Henrik,
>
> Please see the details you required for troubleshooting this problem:
>
> verbose output of the error:
>
>> #Summarization
>>
>> cesList<- li
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