[BioC] error in matchprobes package

[James W. MacDonald]

Hi Yan,

I have no idea why you were having problems with this, unless you didn't 
upgrade to R-devel like I suggested. I didn't have any problems building 
this package.

Rather than trying to talk you through building this yourself, I have 
put it up for download:

http://www.umich.edu/~jmacdon/ehis1a520285fprobe_0.0.1.tar.gz

Best,

Jim



yzhang at vbi.vt.edu wrote:
> Jim:
> 
> I put my cdf and probesequence file and one cel file at the following url.
> if you are willing to repeat my problem, you could download them and try
> in your machine.
> http://ci.vbi.vt.edu/yan/newcdf/huber.html
> Thanks a lot.
> yan
> 
> 
> On Wed, September 12, 2007 4:01 pm, James W. MacDonald wrote:
> 
>> Yan Zhang wrote:
>>
>>> jim:
>>>
>>>
>>> I am wrong. That chip did have MM. I just checked it using mm function
>>> in affy package. The reason that I think it is only has pm is because
>>> only pm in probesequence file.  Then, do you have some suggestion to
>>> solve that error message?
>> Sure. You have two choices. You can add comparewithcdf=FALSE to your
>> call to makeProbePackage(), which will eliminate the warnings because you
>> will no longer be comparing to the cdf. This is the simplest answer, but
>> regrettably the most dangerous as well.
>>
>> Otherwise, you could
>>
>>
>> debug(.lgExtraParanoia)
>>
>> before running makeProbePackage(), and then step through that function,
>> looking at what you get for pm1, mm1, pm2, and mm2 to see why you are
>> getting the error in the first place. I have to assume one of those
>> variables is ending up as an NA (usually this happens because there aren't
>> any MMs). Then you will have to figure out what to do with this
>> information.
>>
>> Best,
>>
>>
>> Jim
>>
>>
>>
>>> best yan
>>>
>>> James W. MacDonald wrote:
>>>
>>>
>>>> Hi Yan,
>>>>
>>>>
>>>> First, please don't take things off-list. The archives are intended
>>>> to be a resource, and if the questions/answers become private then we
>>>> have less of a resource.
>>>>
>>>> Yan Zhang wrote:
>>>>
>>>>
>>>>> Thank you very much for your response.
>>>>> Yes, that chip only has PM. Then, what can I do?
>>>>> I need to solve this problem in order to continue.
>>>>> For warning message,
>>>>> Can I just ignore that warning messages? I doubled. Because later,
>>>>> when I using GCRMA, those NA will cause trouble in the
>>>>> compute.infinite function. What can I do? Can I just delete the head
>>>>> of probesequence file?
>>>>
>>>> You won't be able to do GCRMA with a PM-only chip. GCRMA uses the MM
>>>> probes to compute a background estimate, and if you don't have MM
>>>> probes you won't be able to do that.
>>>>
>>>> As for the second question (which is a moot point now), you don't
>>>> want to delete the head of the probe_tab file. As I mentioned in my
>>>> earlier reply you would need to use the devel version of matchprobes
>>>> with R-2.6.0alpha.
>>>>
>>>>
>>>> Best,
>>>>
>>>>
>>>> Jim
>>>>
>>>>
>>>>
>>>>> best yan
>>>>>
>>>>> James W. MacDonald wrote:
>>>>>
>>>>>
>>>>>> Hi Yan,
>>>>>>
>>>>>>
>>>>>> yzhang at vbi.vt.edu wrote:
>>>>>>
>>>>>>> When I use makeProbePackage function in newest version
>>>>>>> matchprobes package(1.8.1), I got the following error message:
>>>>>>>
>>>>>>>> makeProbePackage("ehis1a520285f",version="1.0",species="ehis"
>>>>>>>> ,maintainer="yanzhang<yzhang at vbi.vt.edu>",build=FALSE,
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> check=FALSE, force=True) Importing the data.
>>>>>>> Error in rep(NA, max(pm1, mm1, pm2, mm2)) :
>>>>>>> invalid 'times' argument In addition: Warning messages:
>>>>>>> 1: NAs introduced by coercion in: as.integer.default(dat[[2]])
>>>>>>> 2: NAs introduced by coercion in: as.integer.default(dat[[3]])
>>>>>>> 3: NAs introduced by coercion in: as.integer.default(dat[[4]])
>>>>>>>
>>>>>>
>>>>>>
>>>>>> The error comes from code that compares the probeset IDs from the
>>>>>>  probe package with the cdf package, and IIRC this happens when
>>>>>> you have a PM-only chip. Is this chip PM-only?
>>>>>>
>>>>>> The warnings come from an unfortunate change that was made to
>>>>>> getProbeDataAffy() that I have fixed in the devel version (and
>>>>>> have no idea right now why I didn't push to the release as
>>>>>> well...). The problem stems from the fact that you are reading in
>>>>>> the whole probe_tab file, including the header. When the (x,y)
>>>>>> coordinates and probe interrogation position data are coerced to
>>>>>> integer, the first value for each is character, which is coerced
>>>>>> to a NA.
>>>>>>
>>>>>> The release branch is no longer being built, so I cannot push a
>>>>>> fix that will end up being available. The easiest thing for you to
>>>>>> do is upgrade your R to 2.6.0 alpha and use the devel version of
>>>>>> matchprobes.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>>
>>>>>> Jim
>>>>>>
>>>>>>
>>>>>>
>>>>>>> I don't have this problem if I use old version(1.0.22).
>>>>>>> Anyonne knows what cause this?
>>>>>>>
>>>>>>>
>>>>>>> best yan
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
>>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives:
>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conducto
>>>>>>> r
>>>>>>
>>>>>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
>>
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623