topTable() in limma packages returns the row numbers and it would be
useful to see the row names (i.e. Affy ID) instead. I am aware that I
may supply the 'genelist' argument but help("topTable") says :
genelist: data frame or character vector containing gene
information. If not specified, this will be taken
from the 'genes' component of 'fit'.
My usual usage is as follows
fit <- lmFit(onebatch, design)
fit2 <- contrasts.fit( fit, cont.m )
fit2 <- eBayes(fit2)
topTable(fit2)
M t P.Value B
12358 -0.8636721 -7.585040 3.808592e-05 11.958486
48048 -0.8765769 -7.400093 7.417187e-05 11.363358
...
But I found no genes component in fit via fit$genes or str(fit). Same
goes for fit2. I doing something wrong ?
Thank you.
Regards, Adai
> Date: Fri, 25 Feb 2005 11:33:57 +0000
> From: Adaikalavan Ramasamy <ramasamy@cancer.org.uk>
> Subject: [BioC] rownames in topTable and posterior probability
> To: BioConductor mailing list <bioconductor@stat.math.ethz.ch>
>
> topTable() in limma packages returns the row numbers and it would be
> useful to see the row names (i.e. Affy ID) instead.
topTable() already does this, as can be seen from the case studies in
the User's Guide. For
example, the Ecoli and Estrogen case studies show top tables with Affy
IDs included automatically.
> I am aware that I
> may supply the 'genelist' argument but help("topTable") says :
>
> genelist: data frame or character vector containing gene
> information. If not specified, this will be taken
> from the 'genes' component of 'fit'.
This is not normally required. Have you not looked at the examples in
the User's Guide?
> My usual usage is as follows
>
> fit <- lmFit(onebatch, design)
> fit2 <- contrasts.fit( fit, cont.m )
> fit2 <- eBayes(fit2)
>
> topTable(fit2)
> M t P.Value B
> 12358 -0.8636721 -7.585040 3.808592e-05 11.958486
> 48048 -0.8765769 -7.400093 7.417187e-05 11.363358
> ...
>
> But I found no genes component in fit via fit$genes or str(fit).
Same
> goes for fit2. I doing something wrong ?
You haven't told use what sort of object 'onebatch' is. If onebatch
is an object from which gene
names can be extracted, e.g., an exprSet, then they should be included
in 'fit'. If 'onebatch'
doesn't include gene names, you can't really expect them to be in fit.
Gordon
> Thank you.
>
> Regards, Adai
Hi,
Where can I get Hu6800 annotation files and the probe
target sequences. I cannot find these at NetAffx site.
Is there any way, I can get target sequences as FASTA
formatted files?
Thanks
S. Peri
S Peri wrote:
> Hi,
> Where can I get Hu6800 annotation files and the probe
> target sequences. I cannot find these at NetAffx site.
The Hu6800 is also known as the HuGeneFl chip.
http://www.affymetrix.com/support/technical/byproduct.affx?product=hug
enefl
HTH,
Jim
>
>
> Is there any way, I can get target sequences as FASTA
> formatted files?
>
> Thanks
> S. Peri
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623
**********************************************************
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues.
Thank you Dr. Symth (and Dr. MacDonald).
As you have correctly suspected, the problem is with the input
'onebatch' which is a matrix. The matrix was actually extracted from
the
exprSet during an intermediate step, stored and used for subsequent
analysis here.
Is it a sensible suggestion for the lmFit() to set the rownames of the
matrix as the gene names _if_ the class of object was matrix ? Might
try
later today to fudge to include a branch for is(object, "matrix") in
the
existing lmFit() code and post it. But is this worth the effort ?
I presume there might be a few people who prefer to work with matrix
of
gene expression. E.g. those who only get the finalised dataset as the
output of some public repositories. Or is it easier to convert a
matrix
to an exprSet and work from there ?
Thank you.
Regards, Adai
On Sun, 2005-02-27 at 00:11 +1100, Gordon K Smyth wrote:
> > Date: Fri, 25 Feb 2005 11:33:57 +0000
> > From: Adaikalavan Ramasamy <ramasamy@cancer.org.uk>
> > Subject: [BioC] rownames in topTable and posterior probability
> > To: BioConductor mailing list <bioconductor@stat.math.ethz.ch>
> >
> > topTable() in limma packages returns the row numbers and it would
be
> > useful to see the row names (i.e. Affy ID) instead.
>
> topTable() already does this, as can be seen from the case studies
in the User's Guide. For
> example, the Ecoli and Estrogen case studies show top tables with
Affy IDs included automatically.
>
> > I am aware that I
> > may supply the 'genelist' argument but help("topTable") says :
> >
> > genelist: data frame or character vector containing gene
> > information. If not specified, this will be taken
> > from the 'genes' component of 'fit'.
>
> This is not normally required. Have you not looked at the examples
in the User's Guide?
>
> > My usual usage is as follows
> >
> > fit <- lmFit(onebatch, design)
> > fit2 <- contrasts.fit( fit, cont.m )
> > fit2 <- eBayes(fit2)
> >
> > topTable(fit2)
> > M t P.Value B
> > 12358 -0.8636721 -7.585040 3.808592e-05 11.958486
> > 48048 -0.8765769 -7.400093 7.417187e-05 11.363358
> > ...
> >
> > But I found no genes component in fit via fit$genes or str(fit).
Same
> > goes for fit2. I doing something wrong ?
>
> You haven't told use what sort of object 'onebatch' is. If onebatch
is an object from which gene
> names can be extracted, e.g., an exprSet, then they should be
included in 'fit'. If 'onebatch'
> doesn't include gene names, you can't really expect them to be in
fit.
>
> Gordon
>
> > Thank you.
> >
> > Regards, Adai
>
>
>
At 01:45 PM 28/02/2005, Adaikalavan Ramasamy wrote:
>Thank you Dr. Symth (and Dr. MacDonald).
>
>As you have correctly suspected, the problem is with the input
>'onebatch' which is a matrix. The matrix was actually extracted from
the
>exprSet during an intermediate step, stored and used for subsequent
>analysis here.
>
>Is it a sensible suggestion for the lmFit() to set the rownames of
the
>matrix as the gene names _if_ the class of object was matrix ? Might
try
>later today to fudge to include a branch for is(object, "matrix") in
the
>existing lmFit() code and post it. But is this worth the effort ?
That's a sensible suggestion which is easy to implement. I'll put it
in the
next version of limma.
>I presume there might be a few people who prefer to work with matrix
of
>gene expression. E.g. those who only get the finalised dataset as the
>output of some public repositories.
In the case of public repositories, I doubt that the matrix will have
rownames attached.
Rownames are not in general a satisfactory way to store probe IDs
because
of the embarassment that non-unique rownames can potentially cause.
The
exprSet class gets away with storing probe IDs this way because
exprSet is
mostly used for Affy and Affy chips don't repeat probes.
Gordon
> Or is it easier to convert a matrix
>to an exprSet and work from there ?
>
>Thank you.
>Regards, Adai
