[BioC] error in matchprobes package
Yan Zhang
yzhang at vbi.vt.edu
Fri Sep 14 14:59:14 CEST 2007
Saroj:
I think you are talking about is an old issue.
I already edited probesequence file and removed those mismatched
probeset ID. Right now, they are matched to each other. Then, I used
matched CDF and probesequence files to generate packages using R2.6
alpha. When I run GCRMA, I still got this error message.
Adjusting for optical effect..Done.
Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
NAs are not allowed in subscripted assignments
That is the reason that I sent e-mail to Dr. Wu and bioconductor list
asked for further help.
We could discuss this issue sometime today.
best
yan
smohapat at vbi.vt.edu wrote:
>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
>>>>>>>>>Bioconductor at stat.math.ethz.ch
>>>>>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>>>Search the archives:
>>>>>>>>>http://news.gmane.org/gmane.science.biology.informatics.cond
>>>>>>>>>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
>>
>>
>>_______________________________________________
>>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.conductor
>>
>>
>>
>>
>
>
>
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