converting probe to gene level
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viritha kaza ▴ 580
@viritha-kaza-4318
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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
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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 10 days ago
Australia/Melbourne/Olivia Newton-John …
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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