Question: arrayQualityMetrics subscript out of bounds error and Harshlight error
0
gravatar for Matthew McCormack
7.9 years ago by
United States
Matthew McCormack180 wrote:
I get the following error when I run arrayQualityMetircs on an affybatch file that has 13 Affymetrix CEL files: Error in .local(object, ...) : subscript out of bounds The full command is: arrayQualityMetrics(expressionset = abatch, outdir = "AQM_GT_Jos5236-5248_Dec_11", force = TRUE, do.logtransform = TRUE) I also get the following error when running Harshlight on the same affy batch file: Error in indices2xy(i, nr = object at nrow) : Indices must start at 0 or 1 (please refer to the help file) ! I thought I would add the Harshlight error, because I'll bet the two are related. I did not generate the .CEL files. I received them and put them into an affy batch file with the command abatch <- ReadAffy() Any ideas as to what the problem is ? Matthew The information in this e-mail is intended only for the ...{{dropped:11}}
affy harshlight • 800 views
ADD COMMENTlink modified 7.9 years ago by Wolfgang Huber13k • written 7.9 years ago by Matthew McCormack180
Answer: arrayQualityMetrics subscript out of bounds error and Harshlight error
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gravatar for Wolfgang Huber
7.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Matthew Thank you for the report. It is difficult to say what is going on without more details. In general, please always make sure you are using the latest versions of Bioconductor, and include the output of sessionInfo(). Beyond that, in order to diagnose/fix your problem, we would need an R script that reproduces the error, and the necessary CEL files (maybe one or two already suffice?) or the AffyBatch object. Best wishes Wolfgang On 12/6/11 10:59 PM, Matthew McCormack wrote: > I get the following error when I run arrayQualityMetircs on an affybatch > file that has 13 Affymetrix CEL files: > Error in .local(object, ...) : subscript out of bounds > > The full command is: > arrayQualityMetrics(expressionset = abatch, outdir = > "AQM_GT_Jos5236-5248_Dec_11", force = TRUE, do.logtransform = TRUE) > > I also get the following error when running Harshlight on the same affy > batch file: > Error in indices2xy(i, nr = object at nrow) : > Indices must start at 0 or 1 (please refer to the help file) ! > > I thought I would add the Harshlight error, because I'll bet the two are > related. I did not generate the .CEL files. I received them and put them > into an affy batch file with the command > abatch <- ReadAffy() > > Any ideas as to what the problem is ? > > Matthew > > > The information in this e-mail is intended only for th...{{dropped:19}}
ADD COMMENTlink written 7.9 years ago by Wolfgang Huber13k
Hi Wolfgang, I downloaded the most recent version of arrayQualityMetrics and everything is working fine now. Thanks for writing this very helpful package. Matthew On 12/6/2011 5:24 PM, Wolfgang Huber wrote: > Dear Matthew > > Thank you for the report. It is difficult to say what is going on > without more details. In general, please always make sure you are > using the latest versions of Bioconductor, and include the output of > sessionInfo(). > > Beyond that, in order to diagnose/fix your problem, we would need an R > script that reproduces the error, and the necessary CEL files (maybe > one or two already suffice?) or the AffyBatch object. > > Best wishes > Wolfgang > > > On 12/6/11 10:59 PM, Matthew McCormack wrote: >> I get the following error when I run arrayQualityMetircs on an affybatch >> file that has 13 Affymetrix CEL files: >> Error in .local(object, ...) : subscript out of bounds >> >> The full command is: >> arrayQualityMetrics(expressionset = abatch, outdir = >> "AQM_GT_Jos5236-5248_Dec_11", force = TRUE, do.logtransform = TRUE) >> >> I also get the following error when running Harshlight on the same affy >> batch file: >> Error in indices2xy(i, nr = object at nrow) : >> Indices must start at 0 or 1 (please refer to the help file) ! >> >> I thought I would add the Harshlight error, because I'll bet the two are >> related. I did not generate the .CEL files. I received them and put them >> into an affy batch file with the command >> abatch <- ReadAffy() >> >> Any ideas as to what the problem is ? >> >> Matthew >> >> >> The information in this e-mail is intended only for t...{{dropped:21}}
ADD REPLYlink written 7.9 years ago by Matthew McCormack180
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