On Tue, Apr 15, 2008 at 7:20 AM, Afsaneh <s.maleki-dizaji at="" dcs.shef.ac.uk=""> wrote:
>
>
>
>
> From: Afsaneh [mailto:s.maleki-dizaji at dcs.shef.ac.uk]
> Sent: 15 April 2008 11:23
> To: 'wettenhall at wehi.edu.au'
> Subject: limma for 2 color data
>
>
>
> Dear James,
>
> I was trying to use limmaPackge,
>
>
>
> Here is my description file, at the moment I have got only one
experiment.
>
>
> SlideNumber
>
> FileNameCy5
>
> FileNameCy3
>
> Cy3
>
> Cy5
>
>
> 1
>
> Imagene2.txt
>
> Inagene1.txt
>
> Wt
>
> Mutant
>
>
>
>
>
> The problem is after normalization when I try to run
>
> fit = lmFit(MA,design= c(1)) ok
>
>
>
> > topTable(fit)
>
> Error in dim(data) <- dim : attempt to set an attribute on NULL
>
>
>
> efit <- eBayes(fit) ??
>
>
>
> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim
=
> stdev.coef.lim) :
>
> No residual degrees of freedom in linear model fits
Hi, Afsaneh.
You will not be able to do statistics with only one sample. The best
you can do is to order your genes by fold change. The error message
above essentially tells you that, but in stats terms.
Sean
> tops = topTable(efit,coef=1,adjust='fdr',sort.by='B',number =
50000)
>
> I would really appreciate if let me know what is the problem.
On Tue, Apr 15, 2008 at 8:03 AM, Afsaneh <s.maleki-dizaji at="" dcs.shef.ac.uk=""> wrote:
> Dear Sean,
> Thanks for reply but when I try,
> > topTable(MA,sort.by='M')
>
> Error in dim(data) <- dim : attempt to set an attribute on NULL
topTable() will not work on an MAList.
> I get error, so how can I get top 10 expressed genes.
You can take the ratio of red/green (or green/red) and order those
ratios from greatest to least.
Sean
On Tue, Apr 15, 2008 at 8:26 AM, Afsaneh <s.maleki-dizaji at="" dcs.shef.ac.uk=""> wrote:
> Thanks, but the problem is how to order and also do you know how can
I replace NA (missing value) with 0 or delete them.
Afsaneh,
It is best to reply to the list so that everyone can benefit from your
questions.
See the order() function for ordering. I would simply ignore the NAs,
as they will be placed "last" by order. Again, see the help for
order() for more details.
Sean
>
> -----Original Message-----
> From: seandavi at gmail.com [mailto:seandavi at gmail.com] On
Behalf Of Sean Davis
> Sent: 15 April 2008 13:12
> To: Afsaneh
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] FW: limma for 2 color data
>
> On Tue, Apr 15, 2008 at 8:03 AM, Afsaneh <s.maleki-dizaji at="" dcs.shef.ac.uk=""> wrote:
> > Dear Sean,
> > Thanks for reply but when I try,
> > > topTable(MA,sort.by='M')
> >
> > Error in dim(data) <- dim : attempt to set an attribute on NULL
>
> topTable() will not work on an MAList.
>
> > I get error, so how can I get top 10 expressed genes.
>
> You can take the ratio of red/green (or green/red) and order those
> ratios from greatest to least.
>
> Sean
>
>
