lumi: target ids versus probe ids?
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@michal-blazejczyk-2231
Last seen 10.3 years ago
Hello, I have a question regarding best practices of the analysis of Illumina data using lumi, more specifically - regarding targets vs probes. In noticed that when I import probe-level data using lumiR(), and them normalize them, I still end up with probe-level data. Are there any "summarization" methods for Illumina data? I mean, when I have expression values for multiple probes from the same target, how should I treat them? The "gene profile" format in BeadStudio simply takes a mean of all probes that come from the same target. Is this the right thing to do? Should it be done before or after normalisation? Or should I ignore target ids when I have probe-level data? Best regards, Michal Blazejczyk
lumi lumi • 1.4k views
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@sean-davis-490
Last seen 4 months ago
United States
On Thu, May 22, 2008 at 11:30 AM, Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> wrote: > Hello, > > I have a question regarding best practices of the analysis of Illumina > data using lumi, more specifically - regarding targets vs probes. > In noticed that when I import probe-level data using lumiR(), > and them normalize them, I still end up with probe-level data. > Are there any "summarization" methods for Illumina data? I mean, > when I have expression values for multiple probes from the same > target, how should I treat them? The "gene profile" format in > BeadStudio simply takes a mean of all probes that come from the > same target. Is this the right thing to do? Should it be done > before or after normalisation? Or should I ignore target ids > when I have probe-level data? Hi, Michal. You might want to take a look at the beadarray package which has methods for normalizing and summarizing bead-level data. The lumi package is designed for pre-summarized data from beadstudio. The lumi authors could also comment, here. Sean
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Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Thu, May 22, 2008 at 11:30 AM, Michal Blazejczyk > <michal.blazejczyk at="" mail.mcgill.ca=""> wrote: >> Hello, >> >> I have a question regarding best practices of the analysis of Illumina >> data using lumi, more specifically - regarding targets vs probes. >> In noticed that when I import probe-level data using lumiR(), >> and them normalize them, I still end up with probe-level data. >> Are there any "summarization" methods for Illumina data? I mean, >> when I have expression values for multiple probes from the same >> target, how should I treat them? The "gene profile" format in >> BeadStudio simply takes a mean of all probes that come from the >> same target. Is this the right thing to do? Should it be done >> before or after normalisation? Or should I ignore target ids >> when I have probe-level data? > Hi, Michal. You might want to take a look at the beadarray package > which has methods for normalizing and summarizing bead-level data. > The lumi package is designed for pre-summarized data from beadstudio. > The lumi authors could also comment, here. > Sean Hi Sean, Actually, I was inquiring on the difference between probe- and gene-level data. Bead-level data does not really interest me at this point. BeadStudio never displays bead-level data, but it displays both probe-level data and gene-level data. Thanks, Michal
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On Thu, May 22, 2008 at 11:44 AM, Michal Blazejczyk <michal.blazejczyk at="" mail.mcgill.ca=""> wrote: > Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Thu, May 22, 2008 at 11:30 AM, Michal Blazejczyk >> <michal.blazejczyk at="" mail.mcgill.ca=""> wrote: >>> Hello, >>> >>> I have a question regarding best practices of the analysis of Illumina >>> data using lumi, more specifically - regarding targets vs probes. >>> In noticed that when I import probe-level data using lumiR(), >>> and them normalize them, I still end up with probe-level data. >>> Are there any "summarization" methods for Illumina data? I mean, >>> when I have expression values for multiple probes from the same >>> target, how should I treat them? The "gene profile" format in >>> BeadStudio simply takes a mean of all probes that come from the >>> same target. Is this the right thing to do? Should it be done >>> before or after normalisation? Or should I ignore target ids >>> when I have probe-level data? > >> Hi, Michal. You might want to take a look at the beadarray package >> which has methods for normalizing and summarizing bead-level data. >> The lumi package is designed for pre-summarized data from beadstudio. >> The lumi authors could also comment, here. > >> Sean > > > Hi Sean, > > Actually, I was inquiring on the difference between probe- and > gene-level data. Bead-level data does not really interest me > at this point. BeadStudio never displays bead-level data, but > it displays both probe-level data and gene-level data. Ahh, sorry about that. Use the probe-level data, yes. There is not a real advantage that I can think of for summarizing to genes at any point during an analysis, as the probes are potentially measuring different things even though they are supposed to be measuring the same gene expression. Sean
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Mark Dunning ▴ 320
@mark-dunning-1634
Last seen 10.3 years ago
Hi Michal, I would definitely recommend working with the probe-level data rather than the gene-level data. I have seen many examples of genes with multiple probes where the results from different probes can look completely different: one probe can be unexpressed all the time, whereas the other can be differentially expressed. The reason could be that one probe targets multiple isoforms of the gene, whereas the other could be targetting one very specific and rare example. I don't think averaging the two signals is at all useful in such situations. Hope this helps, Mark On Thu, 2008-05-22 at 11:30 -0400, Michal Blazejczyk wrote: > Hello, > > I have a question regarding best practices of the analysis of Illumina > data using lumi, more specifically - regarding targets vs probes. > In noticed that when I import probe-level data using lumiR(), > and them normalize them, I still end up with probe-level data. > Are there any "summarization" methods for Illumina data? I mean, > when I have expression values for multiple probes from the same > target, how should I treat them? The "gene profile" format in > BeadStudio simply takes a mean of all probes that come from the > same target. Is this the right thing to do? Should it be done > before or after normalisation? Or should I ignore target ids > when I have probe-level data? > > Best regards, > Michal Blazejczyk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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