[BioC] error in matchprobes package

Fri Sep 14 12:41:23 CEST 2007

Jim and all,

I have been following the messages online and had a chance to talk with
Yan and look at the error messages yesterday.

I think the problem is caused by a discrepancy between the cdf and
probeseq files that Yan received from his collaborator. As I understand
number of probeset id in probesequence file is more than that in CDF file.
614 probeset ID could not be found in CDF file. Yan, please correct me if
I am wrong.

I am guessing that matchprobes adds NAs for the ids missing in the CDF and
this causes the error during gcrma.

Best,

Saroj

On Thu, September 13, 2007 11:38 am, James W. MacDonald wrote:
> 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="e
>>>>>>>>> his"
>>>>>>>>> ,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
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>>>>>>>> ucto 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
>
>
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