Dear Jonathan,

Maybe it helps to see that my both sample and input information are now
effectively RangedData objects

IRanges_JKA
RangedData with 3850192 rows and 1 value column across 25 spaces
           space         ranges   | strand
        <factor>      <IRanges>   |  <Rle>
1           chr1 [10071, 10120]   |      +
2           chr1 [10074, 10123]   |      +
3           chr1 [10075, 10124]   |      +
4           chr1 [10075, 10124]   |      -
5           chr1 [10106, 10155]   |      -
6           chr1 [10147, 10196]   |      -
7           chr1 [10148, 10197]   |      +
8           chr1 [10149, 10198]   |      +
9           chr1 [10150, 10199]   |      +
...          ...            ... ...    ...
3850184     chrM [16491, 16540]   |      -
3850185     chrM [16496, 16545]   |      -
3850186     chrM [16499, 16548]   |      +
3850187     chrM [16502, 16551]   |      +
3850188     chrM [16506, 16555]   |      -
3850189     chrM [16507, 16556]   |      +
3850190     chrM [16515, 16564]   |      -
3850191     chrM [16516, 16565]   |      -
3850192     chrM [16521, 16570]   |      +

IRanges_JKA_I
RangedData with 6443227 rows and 1 value column across 25 spaces
           space         ranges   | strand
        <factor>      <IRanges>   |  <Rle>
1           chr1 [10073, 10122]   |      -
2           chr1 [10165, 10214]   |      +
3           chr1 [10445, 10494]   |      +
4           chr1 [13064, 13113]   |      +
5           chr1 [16060, 16109]   |      +
6           chr1 [16416, 16465]   |      -
7           chr1 [20103, 20152]   |      +
8           chr1 [20103, 20152]   |      +
9           chr1 [51428, 51477]   |      -
...          ...            ... ...    ...
6443219     chrM [16509, 16558]   |      +
6443220     chrM [16511, 16560]   |      -
6443221     chrM [16512, 16561]   |      +
6443222     chrM [16513, 16562]   |      -
6443223     chrM [16516, 16565]   |      +
6443224     chrM [16516, 16565]   |      -
6443225     chrM [16517, 16566]   |      +
6443226     chrM [16518, 16567]   |      -
6443227     chrM [16520, 16569]   |      -


On Wed, Jul 20, 2011 at 4:00 PM, Andreia Fonseca
<andreia.fonseca@gmail.com>wrote:

> Hi Jonathan,
>
> thanks for the help, I have another error now! I have changed the code as
> you suggested and I also spotted that in bayespeak I was calling the bam
> object instead of the IRanges object, still the IRanges object is not proper
> as you mentioned. I manage to create a RangeData object but :
>
>
> #call libraries
> library(GenomicRanges)
> library(BayesPeak)
> library(ShortRead)
> library(chipseq)
> library(ChIPpeakAnno)
> library(multicore)
> library(GenomicFeatures)
>
> #read sample JKA
> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA<-readBamGappedAlignments(JKA)
> GIRanges_JKA<-as(Granges_JKA, "GRanges")
> IRanges_JKA<-as(GIRanges_JKA, "RangedData")
>
>
> #read Input JKA
> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM",
> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
> GIRanges_JKA_I<-as(Granges_JKA_I, "GRanges")
> IRanges_JKA_I<-as(GIRanges_JKA_I, "RangedData")
>
>
> #Peak Calling with BayesPeak
> raw.output <- bayespeak(treatment=IRanges_JKA,
> control=IRanges_JKA_I,use.multicore = TRUE, mc.cores = 4)
>
> error message
>
> Error in `[.default`(space(bed), sel) : invalid subscript type 'S4'
>
> any idea?
> thanks
>
>
>
>
> On Wed, Jul 20, 2011 at 3:38 PM, Jonathan Cairns <
> Jonathan.Cairns@cancer.org.uk> wrote:
>
>> Hi Andreia,
>>
>> On the line "IRanges_JKA<-ranges(Granges_JKA)", you are converting a
>> genomicRanges object to an IRanges object. BayesPeak accepts a RangedData
>> object, as opposed to an IRanges object (in order to retain chromosome
>> information). Replace
>>
>> IRanges_JKA<-ranges(Granges_JKA)
>>
>> with
>>
>> IRanges_JKA<-as(Granges_JKA, "RangedData")
>>
>> and it should run properly.
>>
>> Hope this helps,
>>
>> Jonathan
>>
>>
>> P.S. additionally, the line Library(BayesPeak) should be
>> library(BayesPeak) - you obviously know this, else you wouldn't be getting
>> the correct sessionInfo(), but I point this out in case anybody else tries
>> to run the code...
>>
>> ________________________________________
>> From: Andreia Fonseca [andreia.fonseca@gmail.com]
>> Sent: 20 July 2011 15:24
>> To: Jonathan Cairns; bioconductor
>> Subject: error in bayespeak function
>>
>> Dear all,
>>
>> I am analyzing chipseq data and I am trying to use bayespeak package for
>> peak detection.
>> The code that I am using is
>>
>> #call libraries
>> library(GenomicRanges)
>> Library(BayesPeak)
>> library(ShortRead)
>> library(chipseq)
>> library(ChIPpeakAnno)
>> library(multicore)
>> library(GenomicFeatures)
>>
>> #read sample JKA
>> JKA<-asBam("110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA<-readBamGappedAlignments(JKA)
>> IRanges_JKA<-ranges(Granges_JKA)
>>
>> #read Input JKA
>> JKA_I<-asBam("110402_SN365_B_s_2_seq_GQG-2.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM",
>> overwrite=TRUE,destination="110402_SN365_B_s_2_seq_GQG-1.txt_TABLE_filtered.txt_unique_forfastq.fastq_SAM_BAM")
>> Granges_JKA_I<-readBamGappedAlignments(JKA_I)
>> IRanges_JKA_I<-ranges(Granges_JKA_I)
>>
>> #Peak Calling with BayesPeak
>> raw.output <- bayespeak(treatment=JKA, control=JKA_I,use.multicore = TRUE,
>> mc.cores = 4)
>>
>> after the last command I am getting the forllowing error:
>> Error in substring(temp[1], 1, 5) : invalid multibyte string at '<ed>'
>>
>> I also tried to remove the use of parallelization but the error remains
>> the same, can someone tell me what I am doing wrong ?
>> thanks for the help,
>> Andreia
>>
>> bellow is the information concerning sessionInfo
>>
>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] BayesPeak_1.4.0                     GenomicFeatures_1.4.3
>>  [3] multicore_0.1-5                     ChIPpeakAnno_1.8.0
>>  [5] limma_3.8.2                         org.Hs.eg.db_2.5.0
>>  [7] GO.db_2.4.1                         RSQLite_0.9-1
>>  [9] DBI_0.2-5                           AnnotationDbi_1.14.1
>> [11] BSgenome.Ecoli.NCBI.20080805_1.3.17 multtest_2.8.0
>> [13] Biobase_2.12.2                      biomaRt_2.8.1
>> [15] chipseq_1.2.0                       BSgenome_1.20.0
>> [17] ShortRead_1.10.4                    Rsamtools_1.4.2
>> [19] lattice_0.19-30                     Biostrings_2.20.1
>> [21] GenomicRanges_1.4.6                 IRanges_1.10.4
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.13.1        hwriter_1.2        MASS_7.3-13        RCurl_1.4-2
>> [5] rtracklayer_1.12.4 splines_2.13.1     survival_2.36-9    tools_2.13.1
>> [9] XML_3.1-0
>>
>>
>> --
>>
>> ---------------------------------------------------------------------------------------------
>> Andreia J. Amaral, PhD
>> BioFIG - Center for Biodiversity, Functional and Integrative Genomics
>> Instituto de Medicina Molecular
>> University of Lisbon
>> Tel: +352 217500000 (ext. office: 28253)
>> email:andreiaamaral@fm.ul.pt<mailto:email%3Aandreiaamaral@fm.ul.pt> ;
>> andreiaamaral@fc.ul.pt<mailto:andreiaamaral@fc.ul.pt>
>>
>>
>> NOTICE AND DISCLAIMER
>> This e-mail (including any attachments) is intended for the above-named
>> person(s). If you are not the intended recipient, notify the sender
>> immediately, delete this email from your system and do not disclose or use
>> for any purpose.
>>
>> We may monitor all incoming and outgoing emails in line with current
>> legislation. We have taken steps to ensure that this email and attachments
>> are free from any virus, but it remains your responsibility to ensure that
>> viruses do not adversely affect you.
>> Cancer Research UK
>> Registered in England and Wales
>> Company Registered Number: 4325234.
>> Registered Charity Number: 1089464 and Scotland SC041666
>> Registered Office Address: Angel Building, 407 St John Street, London EC1V
>> 4AD.
>>
>
>
>
> --
>
> ---------------------------------------------------------------------------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
>
>


-- 
---------------------------------------------------------------------------------------------
Andreia J. Amaral, PhD
BioFIG - Center for Biodiversity, Functional and Integrative Genomics
Instituto de Medicina Molecular
University of Lisbon
Tel: +352 217500000 (ext. office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt

	[[alternative HTML version deleted]]

