[BioC] [R] Bioconductor and R-devel
Seth Falcon
sfalcon at fhcrc.org
Wed Aug 31 18:06:45 CEST 2005
Hi Jennifer,
Thanks for the additional output. Sending on to the bioconductor
list. Please direct further reponses there. Assuming this worked
with the current release version (same data) then seems likely a bug
in devel... Now we need the attention of the maintainer :-)
+ seth
On 31 Aug 2005, lai at lindaspaces.com wrote:
> To answer your previous question, I do realize BioC 1.7 is the
> current devel version. I couldn't get BioC 1.6's affy package to
> compile on R-devel, that's what I took a shot at BioC 1.7, and seems
> to work.
>
> Back to the error messages, I have tried what Seth mentioned, and
> here are the outputs from traceback() and debug().
>
> Thank you for your help!
>
>> ampli.eset<-call.exprs(ampl.data, "mas5")
> Error in call.exprs(ampl.data, "mas5") : object "ampl.data" not
> found
>> ampli.eset<-call.exprs(ampli.data, "mas5")
> Background correcting Retrieving data from AffyBatch...done.
> Computing expression calls... .........................Error in
> FUN(X[[25]], ...) : Expecting 22283 unique probesets, found 22284
>> traceback()
> 5: FUN(X[[25]], ...)
> 4: lapply(as.list(X), FUN, ...)
> 3: sapply(1:length(pms[1, ]), function(x) {
> cat(".")
> .C("GetExpressionLevels", as.double(pms[, x]), as.double(mms[,
> x]), as.character(pns), as.integer(length(mms[, x])),
> as.double(ct), as.double(st), exprs =
> double(length(unique.pns)),
> length(unique.pns), PACKAGE = "simpleaffy")$exprs
> })
> 2: justMAS(x, tgt = sc)
> 1: call.exprs(ampli.data, "mas5")
>
>
>> debug(call.exprs(ampli.data, "mas5"))
> Background correcting Retrieving data from AffyBatch...done.
> Computing expression calls... .........................done.
> scaling to a TGT of 100 ... Scale factor for:
> 0203_YH10_H_MCF7_r1.CEL 0.291660289301555 Scale factor for:
> 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212 Scale factor for:
> 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987 Scale factor for:
> 0203_YH13_H_a100MCF10A_r1.CEL 0.451200408584071 Scale factor for:
> 0203_YH14_H_a10MCF7_r1.CEL 0.385462078301135 Scale factor for:
> 0203_YH15_H_a100MCF7_r2.CEL 0.284974495993646 Scale factor for:
> 0203_YH16_H_a100MCF7_r3.CEL 0.376484877281483 Scale factor for:
> 0203_YH17_H_a100MCF10A_r2.CEL 0.374087365857816 Scale factor for:
> 0203_YH18_H_a100MCF10A_r3.CEL 0.487207458237659 Scale factor for:
> 0203_YH19_H_a10MCF7_r2.CEL 0.413217979158927 Scale factor for:
> 0203_YH20_H_a10MCF7_r3.CEL 0.482703032325383 Scale factor for:
> 0203_YH21_H_a10MCF10A_r1.CEL 0.945369383367095 Scale factor for:
> 0203_YH22_H_a10MCF10A_r2.CEL 1.96143996386198 Scale factor for:
> 0203_YH23_H_a10MCF10A_r3_rescan.CEL 0.841535915879218 Scale factor
> for: 0203_YH24_H_MCF7_r2.CEL 0.347797230296638 Scale factor for:
> 0203_YH25_H_MCF7_r3.CEL 0.318539156900791 Scale factor for:
> 0203_YH26_H_MCF10A_r2.CEL 0.578922233010316 Scale factor for:
> 0203_YH27_H_MCF10A_r3.CEL 0.394833650209601 Scale factor for:
> 0403_YH34_H_a10MCF10A_r4.CEL 1.06804698986081 Scale factor for:
> 0403_YH35_H_a1MCF7_r1_2.CEL 3.5923019165673 Scale factor for:
> 0403_YH36_H_a1MCF7_r2.CEL 3.16130786066591 Scale factor for:
> 0403_YH37_H_a1MCF7_r3_2.CEL 2.01330391697437 Scale factor for:
> 0403_YH38_H_a1MCF10A_r1.CEL 0.923877813008534 Scale factor for:
> 0403_YH39_H_a1MCF10A_r2_2.CEL 2.29265379531566 Scale factor for:
> 0403_YH40_H_a1MCF10A_r3.CEL 4.02474777803345 Error in
> debug(call.exprs(ampli.data, "mas5")) : argument must be a function
>
>
> Sincerely,
> Jennifer
>
>
>
> Prof Brian Ripley wrote:
>
>> On Wed, 31 Aug 2005, Seth Falcon wrote:
>>
>>> Hi Jennifer,
>>>
>>> I'm moving this over to the bioconductor mail list since we are
>>> discussing Bioconductor packages, that would be the best place for
>>> the discussion at this point. Please subscribe and reply there.
>>>
>>> A couple quick comments:
>>>
>>> 1. You do realize BioC 1.7 is the current devel version, right?
>>
>>
>> Jennifer needed to use R-devel to get compilation with PG to work.
>> Now, I realize that BioC lags behind R in development (as it has to
>> respond), but with R 2.2.0 five weeks away, I hope not too far.
>>
>>> 2. After you see the error, try traceback() to get a better idea
>>> of
>>> where things are going wrong. Then you can use debug(someFunc) to
>>> debug in the place where the error occurs. I'm sure the package
>>> maintainers will be most receptive to any bug fixes.
>>>
>>> Best,
>>>
>>> + seth
>>>
>>>
>>> On 31 Aug 2005, lai at lindaspaces.com wrote:
>>>
>>>> Hi, I have built R (current development version) and BioConductor
>>>> 1.7 with portland group compiler on a AMD Opteron. When I ran qc
>>>> assessment on Affymetrix latin square data set, I got the
>>>> following output,
>>>>
>>>> Loading required package: affy Loading required package: Biobase
>>>> Loading required package: tools Welcome to Bioconductor Vignettes
>>>> contain introductory material. To view, simply type:
>>>> openVignette() For details on reading vignettes, see the
>>>> openVignette help page. Loading required package: reposTools
>>>> Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson
>>>> Institute for Cancer Research and funded by CANCER RESEARCH UK.
>>>> http://bioinformatics.picr.man.ac.uk/simpleaffy mailto:
>>>> microarray at picr.man.ac.uk Background correcting Retrieving data
>>>> from AffyBatch...done. Computing expression
>>>> calls... .........................done. scaling to a TGT of 100
>>>> ... Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.291660289301555
>>>> Scale factor for: 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212
>>>> Scale factor for: 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987
>>>> Scale factor for: 0203_YH13_H_a100MCF10A_r1.CEL 0.451200408584071
>>>> Scale factor for: 0203_YH14_H_a10MCF7_r1.CEL 0.385462078301135
>>>> Scale factor for: 0203_YH15_H_a100MCF7_r2.CEL 0.284974495993646
>>>> Scale factor for: 0203_YH16_H_a100MCF7_r3.CEL 0.376484877281483
>>>> Scale factor for: 0203_YH17_H_a100MCF10A_r2.CEL 0.374087365857816
>>>> Scale factor for: 0203_YH18_H_a100MCF10A_r3.CEL 0.487207458237659
>>>> Scale factor for: 0203_YH19_H_a10MCF7_r2.CEL 0.413217979158927
>>>> Scale factor for: 0203_YH20_H_a10MCF7_r3.CEL 0.482703032325383
>>>> Scale factor for: 0203_YH21_H_a10MCF10A_r1.CEL 0.945369712044904
>>>> Scale factor for: 0203_YH22_H_a10MCF10A_r2.CEL 1.96143996386198
>>>> Scale factor for: 0203_YH23_H_a10MCF10A_r3_rescan.CEL
>>>> 0.841535915879218 Scale factor for: 0203_YH24_H_MCF7_r2.CEL
>>>> 0.347795838770919 Scale factor for: 0203_YH25_H_MCF7_r3.CEL
>>>> 0.318539156900791 Scale factor for: 0203_YH26_H_MCF10A_r2.CEL
>>>> 0.578922233010316 Scale factor for: 0203_YH27_H_MCF10A_r3.CEL
>>>> 0.394833650209601 Scale factor for: 0403_YH34_H_a10MCF10A_r4.CEL
>>>> 1.06804698986081 Scale factor for: 0403_YH35_H_a1MCF7_r1_2.CEL
>>>> 3.5923019165673 Scale factor for: 0403_YH36_H_a1MCF7_r2.CEL
>>>> 3.16130786066591 Scale factor for: 0403_YH37_H_a1MCF7_r3_2.CEL
>>>> 2.01330391697437 Scale factor for: 0403_YH38_H_a1MCF10A_r1.CEL
>>>> 0.923881702153984 Scale factor for: 0403_YH39_H_a1MCF10A_r2_2.CEL
>>>> 2.29265379531566 Scale factor for: 0403_YH40_H_a1MCF10A_r3.CEL
>>>> 4.02474777803345 Getting probe level data... Computing p-values
>>>> Doing PMA Calls TEST 1 : time Elapsed = 0 1 20
>>>>
>>>> Background correcting Retrieving data from AffyBatch...done.
>>>> Computing expression calls... .........Error in FUN(X[[9]], ...)
>>>> : Expecting 22283 unique probesets, found 22284
>>>>
>>>>
>>>> Can anyone advise me on how to fix this problem? I was able to
>>>> run the same data set with gcc-compiled R2.1.1 and BioConductor
>>>> 1.6 successfully.
>>>>
>>>>
>>>> Here is the code that I ran, if it helps to diagnose the
>>>> problems.
>>>>
>>>> library(simpleaffy);
>>>> library(affy);
>>>>
>>>> ampli.data <- ReadAffy()
>>>>
>>>> # normalize the data using call.exprs and mas5
>>>> ampli.eset <- call.exprs(ampli.data, "mas5")
>>>>
>>>> # see what data is stored in ampli.eset at description@preprocssing
>>>> names(ampli.eset at description@preprocessing)
>>>>
>>>> # acess each piece of information within
>>>> ampli.eset at description@preprocessing scale factors
>>>> ampli.eset at description@preprocessing$sfs
>>>>
>>>> # filenames so that the scale factors can be related to their
>>>> # chips
>>>> ampli.eset at description@preprocessing$filenames
>>>>
>>>> # tgt is the target intensity each chip was scaled to
>>>> ampli.eset at description@preprocessing$tgt
>>>>
>>>> # which version of the affy package was used
>>>> ampli.eset at description@preprocessing$affyversion
>>>>
>>>> qc.data <- qc(ampli.data, ampli.eset);
>>>>
>>>> slotNames(qc.data);
>>>>
>>>> # scale.factors contains a list of scale factors applied to each
>>>> # chip;
>>>> qc.data at scale.factors
>>>>
>>>> # target is the target intensity that each chip was scaled to
>>>> qc.data at target
>>>>
>>>> # percent.present is a list of the percentage of probesets called
>>>> present on each chip;
>>>> qc.data at percent.present
>>>>
>>>> # average.background, minimum.background, maximum.background are
>>>> # all
>>>> lists detailing
>>>> # the average, minimum and maximum background for each chip;
>>>> qc.data at average.background
>>>>
>>>> # spikes is a matrix containing normalized values for each of the
>>>> # spike
>>>> controls
>>>> colnames(qc.data at spikes)
>>>>
>>>>
>>>>
>>>> Thanks,
>>>> Jennifer
>>>>
>>>> ______________________________________________
>>>> R-help at stat.math.ethz.ch mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
>>>> posting guide! http://www.R-project.org/posting-guide.html
>>>
>>>
>>> ______________________________________________
>>> R-help at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide!
>>> http://www.R-project.org/posting-guide.html
>>>
>>
--
Seth Falcon| sfalcon at fhcrc.org | 206-667-6541
Computational Biology, Fred Hutchinson Cancer Research Center
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