[BioC] error in matchprobes package

[James W. MacDonald]

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: 
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>>>>
>>>>
>>>>
>>

-- 
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