question on easyRNASeq developer version
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@delhommeemblde-3232
Last seen 10.6 years ago
Dear Ren?, The best place to post this - where you would get for sure my attention - is the bioconductor mailing list. The advantage is that other developers/users might be able to help you as your message would have a better visibility to the R/Bioc community. I've actually put that mailing list in Cc. There indeed seem to be a sub-setting error somewhere within the function that parses the read information, or so I guess from your error message. Would it be possible for you to share your EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to upload the file. If that is not possible, can you at least trim your bam file to the smallest size sufficient to reproduce the error and share that excerpt with me? Best, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Sep 20, 2012, at 2:04 PM, Ren? B?ttcher wrote: > Dear Mr. Delhomme, > > I would like to ask for your support concerning a problem I'm facing when using your easyRNASeq package. There seems to be an issue in one of the subfunctions, > however, I am not able to tell which one, as the error message is rather short. > > "Error in mk_singleBracketReplacementValue(x, value) : > 'value' must be a CompressedIntegerList object" > > Please not that I'm trying to follow the example cases you provided and I am currently using the developer version since my alignments require multiple reads length support according to your current stable release. You can find a detailed problem description on Seqanswers, as it seems I am not the only one encountering this problem. > > http://seqanswers.com/forums/showthread.php?t=23477 > > With kind regards, > Ren? B?ttcher
easyRNASeq easyRNASeq • 1.6k views
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Yanju Zhang ▴ 20
@yanju-zhang-5509
Last seen 10.6 years ago
Hi Nico As mentioned in SEQAnswers, I also encountered this problem: > "Error in mk_singleBracketReplacementValue(x, value) : > 'value' must be a CompressedIntegerList object" In my bam files, the reads are with different length. I am expecting the solution. If you need more information, please let me know. Best wishes Yanju [[alternative HTML version deleted]]
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Hi Yanju, Would you be OK with uploading the file that creates the problem on my dropbox? If that's OK, I'll send you a link to it. That would be best for me to reproduce the error. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Sep 21, 2012, at 4:32 PM, Yanju Zhang wrote: > Hi Nico > As mentioned in SEQAnswers, I also encountered this problem: > > "Error in mk_singleBracketReplacementValue(x, value) : > > 'value' must be a CompressedIntegerList object" > > In my bam files, the reads are with different length. > > I am expecting the solution. If you need more information, please let me know. > > > Best wishes > Yanju > >
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Hi Nico, It is fine with me to upload my bam file. Please give me the link. Best wishes Yanju Code + error + sessionInfo > chr.sizes=as.list(seqlengths(Hsapiens)) > bamfiles=dir(getwd(),pattern="*.sorted.bam$") > RNASeq<- easyRNASeq(filesDirectory=getwd(), + organism="Hsapiens", + chr.sizes=chr.sizes, + #readLength=80L, + annotationMethod="biomaRt", + format="bam", + count="genes", + summarization="geneModels", + filenames=bamfiles[1], + outputFormat="RNAseq" + ) Checking arguments... Fetching annotations... Computing gene models... Summarizing counts... Processing test.sorted.bam Updating the read length information. The reads have been trimmed. Minimum length of 50 bp. Maximum length of 80 bp. Error in mk_singleBracketReplacementValue(x, value) : 'value' must be a CompressedIntegerList object In addition: Warning messages: 1: The use of the list for providing chromosome sizes has been deprecated. Use a named numeric vector instead. 2: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, : There are 16696 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want? 3: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it. 4: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : Not all the chromosome names in your chromosome size list 'chr.sizes' are present in your read file(s) (aln or bam). 5: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : The available chromosomes in both your read file(s) (aln or bam) and 'chr.sizes' list were restricted to their common term. These are: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY. > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 easyRNASeq_1.3.14 [3] ShortRead_1.15.11 latticeExtra_0.6-24 [5] RColorBrewer_1.0-5 Rsamtools_1.9.30 [7] DESeq_1.9.14 lattice_0.20-6 [9] locfit_1.5-8 BSgenome_1.25.8 [11] GenomicRanges_1.9.65 Biostrings_2.25.12 [13] IRanges_1.15.44 edgeR_2.99.8 [15] limma_3.12.1 biomaRt_2.13.2 [17] Biobase_2.17.7 genomeIntervals_1.13.3 [19] BiocGenerics_0.3.1 intervals_0.13.3 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.1 DBI_0.2-5 RCurl_1.91-1 [4] RSQLite_0.11.1 XML_3.9-4 annotate_1.34.1 [7] bitops_1.0-4.1 genefilter_1.38.0 geneplotter_1.35.1 [10] grid_2.15.1 hwriter_1.3 splines_2.15.1 [13] stats4_2.15.1 survival_2.36-14 xtable_1.7-0 [16] zlibbioc_1.2.0 On 21 September 2012 16:37, Nicolas Delhomme <delhomme@embl.de> wrote: > Hi Yanju, > > Would you be OK with uploading the file that creates the problem on my > dropbox? If that's OK, I'll send you a link to it. That would be best for > me to reproduce the error. > > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Genome Biology Computational Support > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: nicolas.delhomme@embl.de > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > > > On Sep 21, 2012, at 4:32 PM, Yanju Zhang wrote: > > > Hi Nico > > As mentioned in SEQAnswers, I also encountered this problem: > > > "Error in mk_singleBracketReplacementValue(x, value) : > > > 'value' must be a CompressedIntegerList object" > > > > In my bam files, the reads are with different length. > > > > I am expecting the solution. If you need more information, please let me > know. > > > > > > Best wishes > > Yanju > > > > > > [[alternative HTML version deleted]]
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Dear Yanju, Ren?, I tracked down the error to a Bioc package I depend on. The Bioc developer are working on it now and they'll let me know as soon as they come up with a solution. The good news being that they identified the issue, the bad one being that it might take some time to fix. In the meanwhile, I'll try to come up with a decent work-around. I'll keep you posted. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Sep 21, 2012, at 5:54 PM, Yanju Zhang wrote: > Hi Nico, > > It is fine with me to upload my bam file. Please give me the link. > > Best wishes > Yanju > > Code + error + sessionInfo > > chr.sizes=as.list(seqlengths(Hsapiens)) > > bamfiles=dir(getwd(),pattern="*.sorted.bam$") > > RNASeq<- easyRNASeq(filesDirectory=getwd(), > + organism="Hsapiens", > + chr.sizes=chr.sizes, > + #readLength=80L, > + annotationMethod="biomaRt", > + format="bam", > + count="genes", > + summarization="geneModels", > + filenames=bamfiles[1], > + outputFormat="RNAseq" > + ) > > > > Checking arguments... > Fetching annotations... > Computing gene models... > Summarizing counts... > Processing test.sorted.bam > Updating the read length information. > The reads have been trimmed. > Minimum length of 50 bp. > Maximum length of 80 bp. > Error in mk_singleBracketReplacementValue(x, value) : > 'value' must be a CompressedIntegerList object > In addition: Warning messages: > 1: The use of the list for providing chromosome sizes has been deprecated. Use a named numeric vector instead. > 2: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, : > There are 16696 synthetic exons as determined from your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want? > 3: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : > You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it. > 4: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : > Not all the chromosome names in your chromosome size list 'chr.sizes' are present in your read file(s) (aln or bam). > 5: In fetchCoverage(rnaSeq, format = format, filename = filename, filter = filter, : > The available chromosomes in both your read file(s) (aln or bam) and 'chr.sizes' list were restricted to their common term. > These are: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY. > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 easyRNASeq_1.3.14 > [3] ShortRead_1.15.11 latticeExtra_0.6-24 > [5] RColorBrewer_1.0-5 Rsamtools_1.9.30 > [7] DESeq_1.9.14 lattice_0.20-6 > [9] locfit_1.5-8 BSgenome_1.25.8 > [11] GenomicRanges_1.9.65 Biostrings_2.25.12 > [13] IRanges_1.15.44 edgeR_2.99.8 > [15] limma_3.12.1 biomaRt_2.13.2 > [17] Biobase_2.17.7 genomeIntervals_1.13.3 > [19] BiocGenerics_0.3.1 intervals_0.13.3 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.18.1 DBI_0.2-5 RCurl_1.91-1 > [4] RSQLite_0.11.1 XML_3.9-4 annotate_1.34.1 > [7] bitops_1.0-4.1 genefilter_1.38.0 geneplotter_1.35.1 > [10] grid_2.15.1 hwriter_1.3 splines_2.15.1 > [13] stats4_2.15.1 survival_2.36-14 xtable_1.7-0 > [16] zlibbioc_1.2.0 > > > > > On 21 September 2012 16:37, Nicolas Delhomme <delhomme at="" embl.de=""> wrote: > Hi Yanju, > > Would you be OK with uploading the file that creates the problem on my dropbox? If that's OK, I'll send you a link to it. That would be best for me to reproduce the error. > > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Genome Biology Computational Support > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: nicolas.delhomme at embl.de > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > > > On Sep 21, 2012, at 4:32 PM, Yanju Zhang wrote: > > > Hi Nico > > As mentioned in SEQAnswers, I also encountered this problem: > > > "Error in mk_singleBracketReplacementValue(x, value) : > > > 'value' must be a CompressedIntegerList object" > > > > In my bam files, the reads are with different length. > > > > I am expecting the solution. If you need more information, please let me know. > > > > > > Best wishes > > Yanju > > > > > >
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@renebottcher-5521
Last seen 10.6 years ago
> > Dear Ren?, > > The best place to post this - where you would get for sure my attention - is the bioconductor mailing list. The > advantage is that other developers/users might be able to help you as your message would have a better > visibility to the R/Bioc community. I've actually put that mailing list in Cc. > > There indeed seem to be a sub-setting error somewhere within the function that parses the read > information, or so I guess from your error message. Would it be possible for you to share your > EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to upload the file. If that is not > possible, can you at least trim your bam file to the smallest size sufficient to reproduce the error and > share that excerpt with me? > > Best, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Genome Biology Computational Support > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: nicolas.delhomme at ... > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > On Sep 20, 2012, at 2:04 PM, Ren? B?ttcher wrote: > > > Dear Mr. Delhomme, > > > > I would like to ask for your support concerning a problem I'm facing when using your easyRNASeq package. > There seems to be an issue in one of the subfunctions, > > however, I am not able to tell which one, as the error message is rather short. > > > > "Error in mk_singleBracketReplacementValue(x, value) : > > 'value' must be a CompressedIntegerList object" > > > > Please not that I'm trying to follow the example cases you provided and I am currently using the developer > version since my alignments require multiple reads length support according to your current stable > release. You can find a detailed problem description on Seqanswers, as it seems I am not the only one > encountering this problem. > > > > http://seqanswers.com/forums/showthread.php?t=23477 > > > > With kind regards, > > Ren? B?ttcher > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Dear Nicolas, I ran picard-tools FixMateInformation on my bam-file, however, it did not solve the problem. Additionally, the problem also occurs with another sample, so I will now crop both of these bam-files to reduce their size and still retain reproducibility. If you could provide me with your dropbox folder, I can then upload them for you to test where the bug occurs. Thank you for your support. With kind regards, Ren?
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Hi Ren?, I suppose that's the email you mentioned would be on hold, right? Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Sep 27, 2012, at 10:51 AM, Ren?B?ttcher wrote: >> >> Dear Ren?, >> >> The best place to post this - where you would get for sure my attention - is > the bioconductor mailing list. The >> advantage is that other developers/users might be able to help you as your > message would have a better >> visibility to the R/Bioc community. I've actually put that mailing list in Cc. >> >> There indeed seem to be a sub-setting error somewhere within the function that > parses the read >> information, or so I guess from your error message. Would it be possible for > you to share your >> EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to > upload the file. If that is not >> possible, can you at least trim your bam file to the smallest size sufficient > to reproduce the error and >> share that excerpt with me? >> >> Best, >> >> Nico >> >> --------------------------------------------------------------- >> Nicolas Delhomme >> >> Genome Biology Computational Support >> >> European Molecular Biology Laboratory >> >> Tel: +49 6221 387 8310 >> Email: nicolas.delhomme at ... >> Meyerhofstrasse 1 - Postfach 10.2209 >> 69102 Heidelberg, Germany >> --------------------------------------------------------------- >> >> On Sep 20, 2012, at 2:04 PM, Ren? B?ttcher wrote: >> >>> Dear Mr. Delhomme, >>> >>> I would like to ask for your support concerning a problem I'm facing when > using your easyRNASeq package. >> There seems to be an issue in one of the subfunctions, >>> however, I am not able to tell which one, as the error message is rather > short. >>> >>> "Error in mk_singleBracketReplacementValue(x, value) : >>> 'value' must be a CompressedIntegerList object" >>> >>> Please not that I'm trying to follow the example cases you provided and I am > currently using the developer >> version since my alignments require multiple reads length support according to > your current stable >> release. You can find a detailed problem description on Seqanswers, as it > seems I am not the only one >> encountering this problem. >>> >>> http://seqanswers.com/forums/showthread.php?t=23477 >>> >>> With kind regards, >>> Ren? B?ttcher >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at ... >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > Dear Nicolas, > > I ran picard-tools FixMateInformation on my bam-file, however, it did not solve > the problem. Additionally, the problem also occurs with another sample, so I > will now crop both of these bam-files to reduce their size and still retain > reproducibility. If you could provide me with your dropbox folder, I can then > upload them for you to test where the bug occurs. > > Thank you for your support. > > With kind regards, > Ren? > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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