Question: AgiMicroRna with single channel Agilent Array
0
gravatar for John Lande
8.5 years ago by
John Lande280
John Lande280 wrote:
dear Bioc, I have a simple problem. I just got some Agilent single channel data for miRNA to analyse. I check in BioC repository and found the package AgiMicroRna that seems fits my need, however it seems to me that it can only handle 2 channel experiment. do you know any way to properly handle the data with this package or any other? [[alternative HTML version deleted]]
agimicrorna • 647 views
ADD COMMENTlink modified 8.5 years ago • written 8.5 years ago by John Lande280
Answer: AgiMicroRna with single channel Agilent Array
0
gravatar for Axel Klenk
8.5 years ago by
Axel Klenk940
Switzerland
Axel Klenk940 wrote:
Dear John, you don't say what made you think so but the opposite is true: AgiMicroRna will only work with single channel data. We're using it for exactly that and it is straightforward -- just follow the vignette... Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland From: John Lande <john.lande77 at="" gmail.com=""> To: <bioconductor at="" stat.math.ethz.ch=""> Date: 17.07.2011 10:33 Subject: [BioC] AgiMicroRna with single channel Agilent Array Sent by: bioconductor-bounces at r-project.org dear Bioc, I have a simple problem. I just got some Agilent single channel data for miRNA to analyse. I check in BioC repository and found the package AgiMicroRna that seems fits my need, however it seems to me that it can only handle 2 channel experiment. do you know any way to properly handle the data with this package or any other? [[alternative HTML version deleted]] _______________________________________________ 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 The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
ADD COMMENTlink written 8.5 years ago by Axel Klenk940
Answer: AgiMicroRna with single channel Agilent Array
0
gravatar for John Lande
8.5 years ago by
John Lande280
John Lande280 wrote:
Indeed you are right, I was confused by the fact that the package didn accpted my data. however I found that the Agilent Feature Extraction is different from the one used in the package. the software is version 10.7.3.1. do you think this could be the problem? I found that I miss some columns in the imput file. specifically the "gMeanSignal", but I found "gMedianSignal", so i think it will be fine if I just rename it and gBGUsed, for which I cannot fine any correspondance? thank you very much! On Mon, Jul 18, 2011 at 7:54 AM, <axel.klenk@actelion.com> wrote: > Dear John, > > you don't say what made you think so but the opposite is true: > AgiMicroRna will only work with single channel data. We're > using it for exactly that and it is straightforward -- just follow the > vignette... > > Cheers, > > - axel > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > > From: > John Lande <john.lande77@gmail.com> > To: > <bioconductor@stat.math.ethz.ch> > Date: > 17.07.2011 10:33 > Subject: > [BioC] AgiMicroRna with single channel Agilent Array > Sent by: > bioconductor-bounces@r-project.org > > > > dear Bioc, > > I have a simple problem. I just got some Agilent single channel data for > miRNA to analyse. > > I check in BioC repository and found the package AgiMicroRna that seems > fits > my need, however it seems to me that it can only handle 2 channel > experiment. > > do you know any way to properly handle the data with this package or any > other? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended > recipient, any copying, distribution or any other use of this email is > prohibited and may be unlawful. In such case, you should please notify the > sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by > letter. > Any views expressed in this message are those of the individual sender, > except where the message states otherwise and the sender is authorised to > state them to be the views of the sender's company. For further information > about Actelion please see our website at http://www.actelion.com > > > [[alternative HTML version deleted]]
ADD COMMENTlink written 8.5 years ago by John Lande280
Oh yes, a couple of years/FES versions ago, Agilent introduced that new file format (called "compact", IIRC) by omitting some of their many columns, including some important ones, and unfortunately they made this new format the default. You should be able to fix this by changing some FES setting rather than manually renaming your columns... Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland From: John Lande <john.lande77 at="" gmail.com=""> To: axel.klenk at actelion.com, bioconductor at stat.math.ethz.ch Date: 19.07.2011 17:11 Subject: Re: [BioC] AgiMicroRna with single channel Agilent Array Indeed you are right, I was confused by the fact that the package didn accpted my data. however I found that the Agilent Feature Extraction is different from the one used in the package. the software is version 10.7.3.1. do you think this could be the problem? I found that I miss some columns in the imput file. specifically the "gMeanSignal", but I found "gMedianSignal", so i think it will be fine if I just rename it and gBGUsed, for which I cannot fine any correspondance? thank you very much! On Mon, Jul 18, 2011 at 7:54 AM, <axel.klenk at="" actelion.com=""> wrote: Dear John, you don't say what made you think so but the opposite is true: AgiMicroRna will only work with single channel data. We're using it for exactly that and it is straightforward -- just follow the vignette... Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland From: John Lande <john.lande77 at="" gmail.com=""> To: <bioconductor at="" stat.math.ethz.ch=""> Date: 17.07.2011 10:33 Subject: [BioC] AgiMicroRna with single channel Agilent Array Sent by: bioconductor-bounces at r-project.org dear Bioc, I have a simple problem. I just got some Agilent single channel data for miRNA to analyse. I check in BioC repository and found the package AgiMicroRna that seems fits my need, however it seems to me that it can only handle 2 channel experiment. do you know any way to properly handle the data with this package or any other? [[alternative HTML version deleted]] _______________________________________________ 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 The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com
ADD REPLYlink written 8.5 years ago by Axel Klenk940
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