problems using simpleaffy
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Georg Otto ▴ 510
@georg-otto-956
Last seen 7.3 years ago
Hi bioconductors, I have a problem trying to reproduce the user?s guide of simpleaffy with my own data. I do it like this: > x<-read.affy("covdesc") > x.mas5<-call.exprs(x,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ..........done. scaling to a TGT of 100 ...Scale factor for: 1.CEL 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 Scale factor for: 3.CEL 1.27818905696529e-247 Scale factor for: 4.CEL 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 Scale factor for: 6.CEL 2.37641150479280e-156 Scale factor for: 7.CEL 1.27818905696529e-247 Scale factor for: 8.CEL 1.27818905696529e-247 Scale factor for: 9.CEL 2.37641150479280e-156 Scale factor for: 10.CEL 2.37641150479280e-156 > qc.data<-qc(x, x.mas5) Getting probe level data... Computing p-values Doing PMA Calls Error in FUN(X[[4]], ...) : subscript out of bounds First of all , the Scale factors look pretty odd. Secondly, I have no clue, what the error message means. I would appreciate any hint. I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple-darwin6.8 Best, Georg
probe simpleaffy probe simpleaffy • 644 views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
Hi Georg, The scale factors do indeed look somewhat odd - can you tell me what array type you're looking at, and what OS you're running on? Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Georg Otto Sent: 22 March 2005 21:43 To: bioconductor@stat.math.ethz.ch Subject: [BioC] problems using simpleaffy Hi bioconductors, I have a problem trying to reproduce the user?s guide of simpleaffy with my own data. I do it like this: > x<-read.affy("covdesc") > x.mas5<-call.exprs(x,"mas5") Background correcting Retrieving data from AffyBatch...done. Computing expression calls... ..........done. scaling to a TGT of 100 ...Scale factor for: 1.CEL 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 Scale factor for: 3.CEL 1.27818905696529e-247 Scale factor for: 4.CEL 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 Scale factor for: 6.CEL 2.37641150479280e-156 Scale factor for: 7.CEL 1.27818905696529e-247 Scale factor for: 8.CEL 1.27818905696529e-247 Scale factor for: 9.CEL 2.37641150479280e-156 Scale factor for: 10.CEL 2.37641150479280e-156 > qc.data<-qc(x, x.mas5) Getting probe level data... Computing p-values Doing PMA Calls Error in FUN(X[[4]], ...) : subscript out of bounds First of all , the Scale factors look pretty odd. Secondly, I have no clue, what the error message means. I would appreciate any hint. I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple-darwin6.8 Best, Georg _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Dear Crispin, I use the affymetrix zebrafish array, my OS is Mac OS 10.2.8. Best, Georg On Wednesday, March 23, 2005, at 01:53 PM, Crispin Miller wrote: > Hi Georg, > The scale factors do indeed look somewhat odd - can you tell me what > array type you're looking at, and what OS you're running on? > > Crispin > > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg > Otto > Sent: 22 March 2005 21:43 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] problems using simpleaffy > > Hi bioconductors, > > I have a problem trying to reproduce the user?s guide of simpleaffy > with my own data. I do it like this: > >> x<-read.affy("covdesc") >> x.mas5<-call.exprs(x,"mas5") > Background correcting > Retrieving data from AffyBatch...done. > Computing expression calls... > ..........done. > scaling to a TGT of 100 ...Scale factor for: 1.CEL > 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 > Scale factor for: 3.CEL 1.27818905696529e-247 Scale factor for: 4.CEL > 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 > Scale factor for: 6.CEL 2.37641150479280e-156 Scale factor for: 7.CEL > 1.27818905696529e-247 Scale factor for: 8.CEL 1.27818905696529e-247 > Scale factor for: 9.CEL 2.37641150479280e-156 Scale factor for: 10.CEL > 2.37641150479280e-156 > qc.data<-qc(x, x.mas5) Getting probe level > data... > Computing p-values > Doing PMA Calls > Error in FUN(X[[4]], ...) : subscript out of bounds > > > First of all , the Scale factors look pretty odd. Secondly, I have no > clue, what the error message means. I would appreciate any hint. > > I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple- darwin6.8 > > > Best, > > Georg >
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
Hi Georg, I've not been able to test simpleaffy on Mac OS - I'll try to dig out some zebrafish chips and see what they do on Linux, and get back to you... Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Georg Otto Sent: 23 March 2005 13:29 To: Crispin Miller Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] problems using simpleaffy Dear Crispin, I use the affymetrix zebrafish array, my OS is Mac OS 10.2.8. Best, Georg On Wednesday, March 23, 2005, at 01:53 PM, Crispin Miller wrote: > Hi Georg, > The scale factors do indeed look somewhat odd - can you tell me what > array type you're looking at, and what OS you're running on? > > Crispin > > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg > > Otto > Sent: 22 March 2005 21:43 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] problems using simpleaffy > > Hi bioconductors, > > I have a problem trying to reproduce the user?s guide of simpleaffy > with my own data. I do it like this: > >> x<-read.affy("covdesc") >> x.mas5<-call.exprs(x,"mas5") > Background correcting > Retrieving data from AffyBatch...done. > Computing expression calls... > ..........done. > scaling to a TGT of 100 ...Scale factor for: 1.CEL > 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 > Scale factor for: 3.CEL 1.27818905696529e-247 Scale factor for: 4.CEL > 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 > Scale factor for: 6.CEL 2.37641150479280e-156 Scale factor for: 7.CEL > 1.27818905696529e-247 Scale factor for: 8.CEL 1.27818905696529e-247 > Scale factor for: 9.CEL 2.37641150479280e-156 Scale factor for: 10.CEL > 2.37641150479280e-156 > qc.data<-qc(x, x.mas5) Getting probe level > data... > Computing p-values > Doing PMA Calls > Error in FUN(X[[4]], ...) : subscript out of bounds > > > First of all , the Scale factors look pretty odd. Secondly, I have no > clue, what the error message means. I would appreciate any hint. > > I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple- darwin6.8 > > > Best, > > Georg > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 7.3 years ago
Dear Georg, I've just tried some zebrafish chips and given them a go on my version of simpleaffy (2.10) running on a linux machine. As far as I can tell, the data looks sensible - scale factors are ~0.8 and a quick scatter plot of the expression calls also looks OK. I suspect this is an issue with compiling/running on a Mac - which is something I'm afraid I have no experience of doing... The other issue - with the subscript out of bounds error is due to the GAPDH probeset id being incorrect in the data files with the package... I've fixed that, and I'll post a patched version in the next few days. Regards, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Georg Otto Sent: 23 March 2005 13:29 To: Crispin Miller Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] problems using simpleaffy Dear Crispin, I use the affymetrix zebrafish array, my OS is Mac OS 10.2.8. Best, Georg On Wednesday, March 23, 2005, at 01:53 PM, Crispin Miller wrote: > Hi Georg, > The scale factors do indeed look somewhat odd - can you tell me what > array type you're looking at, and what OS you're running on? > > Crispin > > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg > > Otto > Sent: 22 March 2005 21:43 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] problems using simpleaffy > > Hi bioconductors, > > I have a problem trying to reproduce the user?s guide of simpleaffy > with my own data. I do it like this: > >> x<-read.affy("covdesc") >> x.mas5<-call.exprs(x,"mas5") > Background correcting > Retrieving data from AffyBatch...done. > Computing expression calls... > ..........done. > scaling to a TGT of 100 ...Scale factor for: 1.CEL > 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 > Scale factor for: 3.CEL 1.27818905696529e-247 Scale factor for: 4.CEL > 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 > Scale factor for: 6.CEL 2.37641150479280e-156 Scale factor for: 7.CEL > 1.27818905696529e-247 Scale factor for: 8.CEL 1.27818905696529e-247 > Scale factor for: 9.CEL 2.37641150479280e-156 Scale factor for: 10.CEL > 2.37641150479280e-156 > qc.data<-qc(x, x.mas5) Getting probe level > data... > Computing p-values > Doing PMA Calls > Error in FUN(X[[4]], ...) : subscript out of bounds > > > First of all , the Scale factors look pretty odd. Secondly, I have no > clue, what the error message means. I would appreciate any hint. > > I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple- darwin6.8 > > > Best, > > Georg > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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Dear Crispin, thanks a lot for your answer! > I suspect this is an issue with compiling/running on a Mac - which is > something I'm afraid I have no experience of doing... This seems indeed to be the case. Running the R implementation of mas5 x.mas5 <- call.exprs(x, "mas5-R") gives me decent scale factors. > The other issue - with the subscript out of bounds error is due to the > GAPDH probeset id being incorrect in the data files with the > package... I've fixed that, and I'll post a patched version in the > next few days. > When and where will this patch be available? I downloaded and installed simpleaffy_2.10-1 from the 25th of march from the developmental packages site, but I still get the same error: qc<-qc(x, x.mas5R) Getting probe level data... Computing p-values Doing PMA Calls Error in FUN(X[[4]], ...) : subscript out of bounds Best, Georg >> >> >> -----Original Message----- >> From: bioconductor-bounces@stat.math.ethz.ch >> [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Georg > >> Otto >> Sent: 22 March 2005 21:43 >> To: bioconductor@stat.math.ethz.ch >> Subject: [BioC] problems using simpleaffy >> >> Hi bioconductors, >> >> I have a problem trying to reproduce the user?s guide of simpleaffy >> with my own data. I do it like this: >> >>> x<-read.affy("covdesc") >>> x.mas5<-call.exprs(x,"mas5") >> Background correcting >> Retrieving data from AffyBatch...done. >> Computing expression calls... >> ..........done. >> scaling to a TGT of 100 ...Scale factor for: 1.CEL >> 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 >> Scale factor for: 3.CEL 1.27818905696529e-247 Scale factor for: 4.CEL >> 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 >> Scale factor for: 6.CEL 2.37641150479280e-156 Scale factor for: 7.CEL >> 1.27818905696529e-247 Scale factor for: 8.CEL 1.27818905696529e-247 >> Scale factor for: 9.CEL 2.37641150479280e-156 Scale factor for: 10.CEL >> 2.37641150479280e-156 > qc.data<-qc(x, x.mas5) Getting probe level >> data... >> Computing p-values >> Doing PMA Calls >> Error in FUN(X[[4]], ...) : subscript out of bounds >> >> >> First of all , the Scale factors look pretty odd. Secondly, I have no >> clue, what the error message means. I would appreciate any hint. >> >> I am running simpleaffy 2.10 with R 2.0.1 on powerpc-apple- darwin6.8 >> >> >> Best, >> >> Georg >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -------------------------------------------------------- >
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.3 years ago
Georg Otto <georg.otto@tuebingen.mpg.de> writes: > >> The other issue - with the subscript out of bounds error is due to >> the GAPDH probeset id being incorrect in the data files with the >> package... I've fixed that, and I'll post a patched version in the >> next few days. >> > > When and where will this patch be available? I downloaded and > installed simpleaffy_2.10-1 from the 25th of march from the > developmental packages site, but I still get the same error: > > qc<-qc(x, x.mas5R) > Getting probe level data... > Computing p-values > Doing PMA Calls > Error in FUN(X[[4]], ...) : subscript out of bounds simpleaffy_2.10-1 is the most recent (patched) version. Crispin has sent an additional patch for the affy package, which I received today. I suspect that the error is due to the, as yet, unpatched affy. I should have an updated version available later today. I will send an announcement to the list when it is available. Best, + seth
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