converting probe to gene level
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viritha kaza ▴ 580
@viritha-kaza-4318
Last seen 10.3 years ago
Hi Group, Is there any function which would help in converting data from probe level to gene level by averaging the expression of all the probes corresponding to a gene. For eg: array1 array2 probe 1 Gene 1 2 4 probe 2 Gene 1 4 3 probe 3 Gene 2 5 4 result: array1 array2 Gene1 3 3.5 Gene 2 5 4 Could any one give some ideas to perform this? Thanks, Viritha [[alternative HTML version deleted]]
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@sean-davis-490
Last seen 4 months ago
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On Wed, Jan 12, 2011 at 4:38 PM, viritha kaza <viritha.k@gmail.com> wrote: > Hi Group, > Is there any function which would help in converting data from probe level > to gene level by averaging the expression of all the probes corresponding > to > a gene. > For eg: > array1 array2 > probe 1 Gene 1 2 4 > probe 2 Gene 1 4 3 > probe 3 Gene 2 5 4 > > result: > array1 array2 > Gene1 3 3.5 > Gene 2 5 4 > Could any one give some ideas to perform this? > Hi, Viritha. You might look at the aggregate function. Also, you might want to look at the genefilter package vignette which has some tools for doing filtering, including finding representative probes for a given gene. Sean [[alternative HTML version deleted]]
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Wei Shi ★ 3.6k
@wei-shi-2183
Last seen 3 days ago
Australia/Melbourne
Hi Viritha: You do not need a function, but the code below should do this: For array1: tapply(x$array1, factor(x$genes), mean) # x is a data frame containing the data in your example. Cheers, Wei On Jan 13, 2011, at 8:38 AM, viritha kaza wrote: > Hi Group, > Is there any function which would help in converting data from probe level > to gene level by averaging the expression of all the probes corresponding to > a gene. > For eg: > array1 array2 > probe 1 Gene 1 2 4 > probe 2 Gene 1 4 3 > probe 3 Gene 2 5 4 > > result: > array1 array2 > Gene1 3 3.5 > Gene 2 5 4 > Could any one give some ideas to perform this? > Thanks, > Viritha > > [[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 in this email is confidential and intend...{{dropped:6}}
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I think in general the point of algorithms like rma is that you can do better than a simple average. For example, you might use median polish or at least a robust method such as a trimmed mean. Of course, if you only have 2 or 3 probes per gene, averaging is about the best you can do. Naomi At 05:55 PM 1/12/2011, Wei Shi wrote: >Hi Viritha: > > You do not need a function, but the code below should do this: > >For array1: >tapply(x$array1, factor(x$genes), mean) # x is a data frame >containing the data in your example. > >Cheers, >Wei > >On Jan 13, 2011, at 8:38 AM, viritha kaza wrote: > > > Hi Group, > > Is there any function which would help in converting data from probe level > > to gene level by averaging the expression of all the probes > corresponding to > > a gene. > > For eg: > > array1 array2 > > probe 1 Gene 1 2 4 > > probe 2 Gene 1 4 3 > > probe 3 Gene 2 5 4 > > > > result: > > array1 array2 > > Gene1 3 3.5 > > Gene 2 5 4 > > Could any one give some ideas to perform this? > > Thanks, > > Viritha > > > > [[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 in this email is confidential and inten...{{dropped:11}}
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Hi Wei, Thanks....tapply works!!!!! Have to apply it to my data. Thank u all for suggestions. -Viritha On Wed, Jan 12, 2011 at 5:55 PM, Wei Shi <shi@wehi.edu.au> wrote: > Hi Viritha: > > You do not need a function, but the code below should do this: > > For array1: > tapply(x$array1, factor(x$genes), mean) # x is a data frame containing the > data in your example. > > Cheers, > Wei > > On Jan 13, 2011, at 8:38 AM, viritha kaza wrote: > > > Hi Group, > > Is there any function which would help in converting data from probe > level > > to gene level by averaging the expression of all the probes corresponding > to > > a gene. > > For eg: > > array1 array2 > > probe 1 Gene 1 2 4 > > probe 2 Gene 1 4 3 > > probe 3 Gene 2 5 4 > > > > result: > > array1 array2 > > Gene1 3 3.5 > > Gene 2 5 4 > > Could any one give some ideas to perform this? > > Thanks, > > Viritha > > > > [[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 in this email is confidential and inte...{{dropped:10}}
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On Thu, Jan 13, 2011 at 12:06 PM, viritha kaza <viritha.k@gmail.com> wrote: > Hi Wei, > Thanks....tapply works!!!!! > Have to apply it to my data. > Have a look at the aggregate function. Sean > Thank u all for suggestions. > > -Viritha > > > On Wed, Jan 12, 2011 at 5:55 PM, Wei Shi <shi@wehi.edu.au> wrote: > > > Hi Viritha: > > > > You do not need a function, but the code below should do this: > > > > For array1: > > tapply(x$array1, factor(x$genes), mean) # x is a data frame containing > the > > data in your example. > > > > Cheers, > > Wei > > > > On Jan 13, 2011, at 8:38 AM, viritha kaza wrote: > > > > > Hi Group, > > > Is there any function which would help in converting data from probe > > level > > > to gene level by averaging the expression of all the probes > corresponding > > to > > > a gene. > > > For eg: > > > array1 array2 > > > probe 1 Gene 1 2 4 > > > probe 2 Gene 1 4 3 > > > probe 3 Gene 2 5 4 > > > > > > result: > > > array1 array2 > > > Gene1 3 3.5 > > > Gene 2 5 4 > > > Could any one give some ideas to perform this? > > > Thanks, > > > Viritha > > > > > > [[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 in this email is confidential and inte...{{dropped:10}} > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
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Hi Sean, Sure I will look into that function too. Thanks, Viritha On Thu, Jan 13, 2011 at 4:39 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Thu, Jan 13, 2011 at 12:06 PM, viritha kaza <viritha.k@gmail.com>wrote: > >> Hi Wei, >> Thanks....tapply works!!!!! >> Have to apply it to my data. >> > > Have a look at the aggregate function. > > Sean > > >> Thank u all for suggestions. >> >> -Viritha >> >> >> On Wed, Jan 12, 2011 at 5:55 PM, Wei Shi <shi@wehi.edu.au> wrote: >> >> > Hi Viritha: >> > >> > You do not need a function, but the code below should do this: >> > >> > For array1: >> > tapply(x$array1, factor(x$genes), mean) # x is a data frame containing >> the >> > data in your example. >> > >> > Cheers, >> > Wei >> > >> > On Jan 13, 2011, at 8:38 AM, viritha kaza wrote: >> > >> > > Hi Group, >> > > Is there any function which would help in converting data from probe >> > level >> > > to gene level by averaging the expression of all the probes >> corresponding >> > to >> > > a gene. >> > > For eg: >> > > array1 array2 >> > > probe 1 Gene 1 2 4 >> > > probe 2 Gene 1 4 3 >> > > probe 3 Gene 2 5 4 >> > > >> > > result: >> > > array1 array2 >> > > Gene1 3 3.5 >> > > Gene 2 5 4 >> > > Could any one give some ideas to perform this? >> > > Thanks, >> > > Viritha >> > > >> > > [[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 in this email is confidential and inte...{{dropped:10}} >> >> >> _______________________________________________ >> 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 >> > > [[alternative HTML version deleted]]
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