Hi Tim,

That worked at least in getting the names in the list, although I don't
understand what this grep section is doing? I just want the names in
some.probes?

named <- data.matrix(my.exprs[ some.probes,
                                 grep('CD34', names(my.exprs)) ])

Sadly:

heatmap(named, main='a heatmap')

gives the same error as before:

'x' must have at least 2 rows and 2 columns




On Tue, Feb 15, 2011 at 3:41 PM, Tim Triche, Jr. <ttriche@usc.edu> wrote:

> alternative with probe names as row names (now I remember why it's better
> that way):
>
> > some.probes <- unlist(mget(c('ASXL1','WIT1','DAPK1'),
>                              hgu133plus2ALIAS2PROBE))
> > named <- data.matrix(my.exprs[ some.probes,
>                                  grep('CD34', names(my.exprs)) ])
> > rownames(named) <- make.names( unlist(mget(some.probes,
>                                              hgu133plus2SYMBOL)) )
> > heatmap(named, main='a heatmap')
>
>
>
>
> On Tue, Feb 15, 2011 at 3:10 PM, Pete Shepard <peter.shepard@gmail.com>wrote:
>
>> Hi Tim,
>>
>> Thanks for your response.
>>
>> rownames(dat.n) <- make.names(mget(rownames(dat.n), hgu133a2SYMBOL,
>> ifnotfound=NA))
>>
>> and
>>
>> rownames(dat.n) <- mget(rownames(dat.n), hgu133a2SYMBOL, ifnotfound=NA)
>>
>> seems to give me the same output.
>>
>> dat.plotme <- dat.n[ "NPEPL1",]
>>
>> using this command, I can only enter one gene symbol.
>>
>> If I run:
>>
>> heatmap(dat.plotme)
>>
>> I get the folllowing output:
>>
>> Error in heatmap(dat.plotme) : 'x' must be a numeric matrix
>>
>> Confused here
>>
>> On Tue, Feb 15, 2011 at 1:58 PM, Tim Triche <tim.triche@gmail.com> wrote:
>>
>>> library(hgu133plus2.db)
>>> rownames(dat.n) <- mget(rownames(dat.n), hgu133plus2SYMBOL,
>>>                         ifnotfound=NA)
>>> dat.plotme <- dat.n[ some.symbols, ]
>>> heatmap(dat.plotme)
>>>
>>>
>>> On Tue, Feb 15, 2011 at 1:43 PM, Pete Shepard <peter.shepard@gmail.com>wrote:
>>>
>>>>  Dear List,
>>>>
>>>> I am attempting to visualize some affymetrix data from the hgu133a2.db
>>>> chip
>>>> using heatmap. So far, what I've done is as follows
>>>>
>>>> dat<-ReadAffy(filenames = "GSM448823.CEL",
>>>> "GSM448824.CEL","GSM448816.CEL",
>>>> "GSM448817.CEL")  #puts .CEL files into a data frame
>>>>
>>>> dat2<-rma(dat)          #normalizes data
>>>>
>>>> dat.n<-exprs(dat2)
>>>>
>>>>
>>>> What I would like to do next is for a subset of gene symbols, ~ 10, I
>>>> would
>>>> like to make a heatmap and display the gene symbols instead of the probe
>>>> ids.
>>>>
>>>> So, I need to first get gene symbols from the probe ids and then select
>>>> only
>>>> a subset of these symbols from "dat.n" and make a heatmap of these
>>>> symbols.
>>>>
>>>> Can anyone help me regarding this problem?
>>>>
>>>> Thanks
>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
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>>>> Search the archives:
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>>>>
>>>
>>>
>>>
>>> --
>>> If people do not believe that mathematics is simple, it is only because
>>> they do not realize how complicated life is.
>>> John von Neumann<http://www-groups.dcs.st-and.ac.uk/%7Ehistory/Biographies/Von_Neumann.html>
>>>
>>>
>>
>
>
> --
> Pure reason shows that reason is not enough.
>
> Dennis V. Lindley<http://www.york.ac.uk/depts/maths/histstat/people/lindley.gif>
>
>

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