[BioC] error in matchprobes package

[James W. MacDonald]

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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>>
>>

-- 
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