Zhijin: Thank you very much for identify the problem. yan Zhijin Wu wrote: > I think Saroj is right. The cdf package gives only 153525 pm index, > but there are 158334 probe sequences. So there are some probes with > sequence but the cdf package doesn't have their location. > GCRMA is able to handle the situation that sequence for some probes > are not given (since in the past there are incomplete probe sequence > files), but it expects no more probe sequence than those given in cdf > pkg. > > I could adjust gcrma to take the intersection of what cdf and probe > packages have in common, but I wonder if this discrepancy between cdf > and probe package is something we would expect. > > pmIndex <- unlist(indexProbes(new("AffyBatch", cdfName = > "ehis1a520285f"),"pm")) > length(pmIndex) > [1] 153525 > > p=get("ehis1a520285fprobe")$sequence > > length(p) > [1] 158334 > > > > > Yan Zhang wrote: > >> 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 >>>> >>>> >>>> >>> >>> >>> >>> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> 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 > > >