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Addiel de Alba | 1 Feb 2011 01:37
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Re: exporting mas5 data with xps

cstrato <cstrato <at> ...> writes:

> 
> Dear Addiel,
> 
> Yes, it is the transcript_cluster_id in the Affymetrix annotation, 
> assuming that you have used mas5(...,option = "transcript",..). If you 
> have used mas5(...,option = "probeset",..) then it will be the 
> probeset_id, see ?mas5.
> 
> BTW, can you please always supply your sessionInfo().
> 
> Best regards
> Christian
> 
> On 1/30/11 12:28 AM, Addiel U. de Alba Solis wrote:
> >
> > Dear Christian,
> >
> > I am following the script4exon you provide to process HuEx-1_0-st-v2 data.
> > When exporting after processing and making MAS5 calls:
> >
> >> export.expr(data.x.mas5,
> > varlist="fUnitName:fTranscriptID",outfile="MAS5EXPRLEVELS.txt")
> >
> > The command replies with:
> >
> > NULL , and then exports the text file
> >
> > However instead of having a transcript ID field(label) it has a ProbesetID
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Pedro Lopez-Romero | 1 Feb 2011 11:00
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Re: AgiMicroRna problem

Hi Pablo,

The function "read.maimages" is no longer used by AgimicroRna.
"read.maimages" creates an object of class RGList with element names: R, Rb,
G, Gb, etc ..., that are proper for two-channel arrays. To make the names
more intuitive for the analysis of microRna arrays, I have introduced some
changes and now, AgimicroRna creates an object of class uRNAlist with the
names:

"TGS" for the "gTotalGeneSignal",
"TPS" for the "gTotalProbeSignal",
"meanS" for the "gMeanSignal",
"procS" for the "gProcessedSignal".

If you use "read.maimages" you will create an object that is no longer
available in AgimicroRna, and that´s the error you´ve got.

Please, to read the data use the fucntion:
 readMicroRnaAFE(targets,verbose=FALSE).
Please have a look at the help of readMicroRnaAFE and at the vignette file
(to see the changes)
For a quick look of the new characteristics of AgiMicroRna, please, have a
look as well at: "Lopez-Romero P. Pre-processing and differential expression
analysis of Agilent microRNA arrays
using the AgiMicroRna Bioconductor library. BMC Genomics 2011, 12:64".

p.-

On Sun, Jan 30, 2011 at 1:03 AM, Paulo Nuin <nuin@...> wrote:
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Paulo Nuin | 1 Feb 2011 15:47
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Re: AgiMicroRna problem

Thanks a lot. I will try this.

Cheers
Paulo

On 2011-02-01, at 5:00 AM, Pedro Lopez-Romero wrote:

> 
> Hi Pablo,
>  
> The function "read.maimages" is no longer used by AgimicroRna.
> "read.maimages" creates an object of class RGList with element names: R, Rb, G, Gb, etc ..., that are
proper for two-channel arrays. To make the names more intuitive for the analysis of microRna arrays, I
have introduced some changes and now, AgimicroRna creates an object of class uRNAlist with the names:
> "TGS" for the "gTotalGeneSignal",
> "TPS" for the "gTotalProbeSignal",
> "meanS" for the "gMeanSignal",
> "procS" for the "gProcessedSignal".
> 
> If you use "read.maimages" you will create an object that is no longer available in AgimicroRna, and
that´s the error you´ve got.
> 
> Please, to read the data use the fucntion:  readMicroRnaAFE(targets,verbose=FALSE).
> 
> Please have a look at the help of readMicroRnaAFE and at the vignette file (to see the changes)
> For a quick look of the new characteristics of AgiMicroRna, please, have a look as well at: "Lopez-Romero
P. Pre-processing and differential expression analysis of Agilent microRNA arrays
> using the AgiMicroRna Bioconductor library. BMC Genomics 2011, 12:64".
> p.- 
>
(Continue reading)

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Duke | 1 Feb 2011 16:06
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Re: find overlap of bed files of different length

On 1/31/11 1:20 PM, Kasper Daniel Hansen wrote:
> Use findOverlaps to find all cases.  This is usually the hard and big
> computation.  Then use for example pintersect() to compute the actual
> overlap in percent.  There might be some tedious coding involved.

Thanks for your suggestion Kasper, though honestly I have not tried it 
yet. But based on what Martin and you suggested, I thought the final 
code will not run fast because of extracting to strand/subset and 
running each. Especially my task is a little more complicated: I need to 
find gene expressions (counting sequences in exonic regions of each 
gene). I also gave BEDTools a try, but it does not fulfil my needs 
(extremely slow for a gene list of 28k).

I ended up with coding a c++ code to do the job. Thanks for all of your 
suggestions and helps guys.

D.

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Francesca Buffa | 1 Feb 2011 16:28
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Kasper Daniel Hansen | 1 Feb 2011 18:07
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Re: find overlap of bed files of different length

Well, clearly I have not done it, but I would expect that a decent
implementation of my method would take less than 2 minutes (although
it depends on length of the stuff in the BED file you started with).
At least the computational load should not be much more than running
findOverlaps.

Kasper

On Tue, Feb 1, 2011 at 10:06 AM, Duke <duke.lists@...> wrote:
> On 1/31/11 1:20 PM, Kasper Daniel Hansen wrote:
>>
>> Use findOverlaps to find all cases.  This is usually the hard and big
>> computation.  Then use for example pintersect() to compute the actual
>> overlap in percent.  There might be some tedious coding involved.
>
> Thanks for your suggestion Kasper, though honestly I have not tried it yet.
> But based on what Martin and you suggested, I thought the final code will
> not run fast because of extracting to strand/subset and running each.
> Especially my task is a little more complicated: I need to find gene
> expressions (counting sequences in exonic regions of each gene). I also gave
> BEDTools a try, but it does not fulfil my needs (extremely slow for a gene
> list of 28k).
>
> I ended up with coding a c++ code to do the job. Thanks for all of your
> suggestions and helps guys.
>
> D.
>

_______________________________________________
(Continue reading)

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Ravi Karra | 1 Feb 2011 18:19
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Annotation of Nimblegen Zebrafish Array

Hello all, 

Thank you for maintaining this very informative mailing list.  I am currently working with some gene
expression data using the Nimblegen Zebrafish 12 x135K Expression platform.  Unfortunately, my
analysis has been limited by annotation.  The probes were derived from a variety of sources, many of which
are now out of date. 

A bit reluctantly, I would like to remap the array to the latest zebrafish genome available (Zv9) at Ensembl
so that I can then use biomart for subsequent annotation.  I am able to map most of the probe sequences in the
.ndf file to the Zv9 using matchPDict (basically using a minimally modified version of the code at http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Mapping-of-Affy-Probes-to-Transcrip).

Once I do this, I am stuck.  How can I use these results to make an annotation file with PDInfoBuilder?  How do I
handle probes that do not align with Zv9?  Can I get still use rma?

Thank you in advance.

Ravi
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Sean Davis | 1 Feb 2011 18:36
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Re: Annotation of Nimblegen Zebrafish Array

On Tue, Feb 1, 2011 at 12:19 PM, Ravi Karra <ravi.karra@...> wrote:

> Hello all,
>
> Thank you for maintaining this very informative mailing list.  I am
> currently working with some gene expression data using the Nimblegen
> Zebrafish 12 x135K Expression platform.  Unfortunately, my analysis has been
> limited by annotation.  The probes were derived from a variety of sources,
> many of which are now out of date.
>
> A bit reluctantly, I would like to remap the array to the latest zebrafish
> genome available (Zv9) at Ensembl so that I can then use biomart for
> subsequent annotation.  I am able to map most of the probe sequences in the
> .ndf file to the Zv9 using matchPDict (basically using a minimally modified
> version of the code at
> http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Mapping-of-Affy-Probes-to-Transcrip
> ).
>

Mapping expression probes to the genome is perhaps not the best way to go.
 You should map, instead, to the transcripts.  This is not so big a deal for
25mers (and so the vignette using affy is probably not unjustifiable).
 However, if you are using Nimblegen 50-60mers, then you ought to consider
mapping to the transcripts.  If a probe does not map to a transcript, you
can probably just ignore it.  An alternative is to be more exhaustive and
map to things like ESTs, etc.

>
> Once I do this, I am stuck.  How can I use these results to make an
> annotation file with PDInfoBuilder?  How do I handle probes that do not
(Continue reading)

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Ravi Karra | 1 Feb 2011 18:49
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Re: Annotation of Nimblegen Zebrafish Array

Hi Sean, 
Thanks for your reply.  I should have been more specific.  I am mapping to the Zv9 cDNA build that I have
downloaded from Ensembl.
Best, 
Ravi

On Feb 1, 2011, at 12:36 PM, Sean Davis wrote:

> 
> 
> On Tue, Feb 1, 2011 at 12:19 PM, Ravi Karra <ravi.karra@...> wrote:
> Hello all,
> 
> Thank you for maintaining this very informative mailing list.  I am currently working with some gene
expression data using the Nimblegen Zebrafish 12 x135K Expression platform.  Unfortunately, my
analysis has been limited by annotation.  The probes were derived from a variety of sources, many of which
are now out of date.
> 
> A bit reluctantly, I would like to remap the array to the latest zebrafish genome available (Zv9) at
Ensembl so that I can then use biomart for subsequent annotation.  I am able to map most of the probe
sequences in the .ndf file to the Zv9 using matchPDict (basically using a minimally modified version of
the code at http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-Mapping-of-Affy-Probes-to-Transcrip).
> 
> Mapping expression probes to the genome is perhaps not the best way to go.  You should map, instead, to the
transcripts.  This is not so big a deal for 25mers (and so the vignette using affy is probably not
unjustifiable).  However, if you are using Nimblegen 50-60mers, then you ought to consider mapping to the
transcripts.  If a probe does not map to a transcript, you can probably just ignore it.  An alternative is to
be more exhaustive and map to things like ESTs, etc. 
>  
>
(Continue reading)

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Michael Lawrence | 1 Feb 2011 19:11

Re: find overlap of bed files of different length

On Tue, Feb 1, 2011 at 7:06 AM, Duke <duke.lists@...> wrote:

> On 1/31/11 1:20 PM, Kasper Daniel Hansen wrote:
>
>> Use findOverlaps to find all cases.  This is usually the hard and big
>> computation.  Then use for example pintersect() to compute the actual
>> overlap in percent.  There might be some tedious coding involved.
>>
>
> Thanks for your suggestion Kasper, though honestly I have not tried it yet.
> But based on what Martin and you suggested, I thought the final code will
> not run fast because of extracting to strand/subset and running each.
> Especially my task is a little more complicated: I need to find gene
> expressions (counting sequences in exonic regions of each gene). I also gave
> BEDTools a try, but it does not fulfil my needs (extremely slow for a gene
> list of 28k).
>
> I ended up with coding a c++ code to do the job. Thanks for all of your
> suggestions and helps guys.
>
>
It would be nice to have a little more detail about what you needed. If
findOverlaps and friends aren't doing the job, it would be good to know.
Counting reads in exons of genes is as simple as calling countOverlaps on
the GRangesList of the exons.

>
> D.
>
> _______________________________________________
(Continue reading)

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