Hi
using R 1.8.0
limma 1.5.1
Attempting to use the Kooperberg background correction in Limma
> RGmodel <- kooperberg(FILES, layout=LAYOUT, fg="mean", bg="mean")
&
> RGmodel <- kooperberg(FILES, layout=LAYOUT, fg="median",
bg="median")
both return following error:
Error in integrate(.numeratorBayesianAdjustedFG, ifelse((fg - bg - 4 *
:
a limit is missing
any ideas much appreciated
thanks
Jason
--
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA
Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919
Hi Jason,
> Hi
>
> using R 1.8.0
> limma 1.5.1
>
> Attempting to use the Kooperberg background correction in Limma
> > RGmodel <- kooperberg(FILES, layout=LAYOUT, fg="mean", bg="mean")
>
> &
>
> > RGmodel <- kooperberg(FILES, layout=LAYOUT, fg="median",
bg="median")
>
> both return following error:
>
>
> Error in integrate(.numeratorBayesianAdjustedFG, ifelse((fg - bg - 4
*
> :
> a limit is missing
This means that one of the limits (lower/upper) passed to the function
integrate() is a missing value (NA) for one of the genes. I wouldn't
have
expected this error because the limits are calculated using data from
the
GenePix results files without logging.
Can you check that the columns "F532 Mean", "F532 SD", "B532 Mean",
"B532
SD", "F635 Mean", "F635 SD", "B635 Mean", "B635 SD", "F Pixels" and "B
Pixels" in your files don't have any missing values?
If there are no NA's, perhaps you can send me an example of one of
your
.gpr files so I can take a closer look at the problem. Best wishes,
Matt Ritchie
> any ideas much appreciated
>
> thanks
>
> Jason
>
>
>This means that one of the limits (lower/upper) passed to the
function
>integrate() is a missing value (NA) for one of the genes. I wouldn't
have
>expected this error because the limits are calculated using data from
the
>GenePix results files without logging.
>
>Can you check that the columns "F532 Mean", "F532 SD", "B532 Mean",
"B532
>SD", "F635 Mean", "F635 SD", "B635 Mean", "B635 SD", "F Pixels" and
"B
>Pixels" in your files don't have any missing values?
>
>If there are no NA's, perhaps you can send me an example of one of
your
>.gpr files so I can take a closer look at the problem. Best wishes,
>
>
Hi Matt
One of my gpr files has data from a
top row of a sub grid with values of 0
looking at the original image these spots have been printed right on
the
edge of the possible scan area
where I'm guessing information is being lost when genepix is
extracting
data.
Is there an arbitrary number I could give this small set of spots to
replace the 0's
or would that defeat the object
I've tried the kooperberg approach on other gpr files and they all
work fine
many thanks
Jason
>--
>--------------------------------
>Jason Skelton
>Pathogen Microarrays
>Wellcome Trust Sanger Institute
>Hinxton
>Cambridge
>CB10 1SA
>
>Tel +44(0)1223 834244 Ext 7123
>Fax +44(0)1223 494919
>--------------------------------
>
>
Hi Jason,
> Hi Matt
>
> One of my gpr files has data from a
> top row of a sub grid with values of 0
>
> looking at the original image these spots have been printed right on
the
> edge of the possible scan area
> where I'm guessing information is being lost when genepix is
extracting
> data.
>
> Is there an arbitrary number I could give this small set of spots to
> replace the 0's
Yes, the easiest thing to do is to make up some values for those spots
to
keep the kooperberg() function happy. I'd make a temporary .gpr file
and
replace the relevant rows with complete rows from nearby spots.
> or would that defeat the object
It won't make a lot of difference to the model, as the adaptive
background
correction is done on each channel separately for each spot (there are
a
few shared parameters estimated for each channel across the whole
array,
however these are unlikely to change). You can reset the R, G values
for
the lost spots to missing once kooperberg() has finished.
Sorry about the messy solution. Best wishes,
Matt Ritchie
> I've tried the kooperberg approach on other gpr files and they all
work
> fine
>
> many thanks
>
> Jason
>
>>This means that one of the limits (lower/upper) passed to the
function
>> integrate() is a missing value (NA) for one of the genes. I
wouldn't
>> have expected this error because the limits are calculated using
data
>> from the GenePix results files without logging.
>>
>>Can you check that the columns "F532 Mean", "F532 SD", "B532 Mean",
>> "B532 SD", "F635 Mean", "F635 SD", "B635 Mean", "B635 SD", "F
Pixels"
>> and "B Pixels" in your files don't have any missing values?
>>
>>If there are no NA's, perhaps you can send me an example of one of
your
>> .gpr files so I can take a closer look at the problem. Best
wishes,
