One of the CEL files is truncated or otherwise corrupted. The
appropriate place to really detect that is in the code that reads the
CEL file data and appropriately warn or error to the user.
The bug below occurs because of a massive mismatch between the
assumptions of the RMA background model
One of your cell files is funky
> colSums(exprs(alldata) == 0)
GSM907854.CEL.gz GSM907866.CEL.gz GSM907857.CEL.gz GSM907863.CEL.gz
000 686388
GSM907856.CEL.gz GSM907862.CEL.gz GSM907855.CEL.gz GSM907861.CEL.gz
0
Dear all,
sorry for the delayed response, due to some unfortunate events I had to
prioritize my family the past week.
You find an RStudio project in a zipped folder on this link :
https://jorismeys.stackstorage.com/s/3ik0vMwsvueuT5a
It contains a script called testOligo.R that can be sourced and
How about a google drive? This problem of autodownloading should be
addressed directly.
These facilities are still important but their maintenance is clearly a
lower priority as the
technologies handled have diminished use in the field. I think we should
be able to team up and remove autoinstalla
Thank you for the answer.
I was trying to create a reproducible example before I vented maybe a bit
too much in my previous mail.
I managed to get closer to the problem and it is related to data that was
corrupted at download. I can send you a reproducible example that bombs R,
but I will have to
>
>> The warning I get when trying oligo::read.celfiles() on a single CEL file
>> right after installing it about the pd.hugene.1.0.st.v1 package. The even
>> more annoying thing is that on my machine it insists on building from
>> source, whereas on another Windows machine without Rtools, it downl
I think there are multiple complaints here, so I'll take them one at a time.
On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:
> Joris,
>
> Sorry I don't have much to offer here. I've cc'd the authors of oligo and
> affy who may have some insight.
>
>
Joris,
Sorry I don't have much to offer here. I've cc'd the authors of oligo and affy
who may have some insight.
Valerie
On 05/02/2018 11:35 AM, Joris Meys wrote:
Dear,
I've noticed that using certain functions in affy and oligo (eg
oligo::read.celfiles and affy::bg.correct) start with downl
