[BioC] error in matchprobes package

[Yan Zhang]

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?

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
>>>>
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>>>
>>>
>>>
>