Hi,
Is there a way of extracting ONLY a list of the attributes of an
output file
from the siggenes package?
After doing a sam calculation:
>A.out <- sam(AE0627999.data, AE0627999.cl,
B=200,rand=123,gene.names=matrix_all_names[,2])
I wanted than to look at the attributes of the file:
>attributes(A.out)
The List I've got is to long to be observed in my GUI window, so I
would like to
know, if there is a possibility to only see the titles of the
attributes and not
the whole list.
THX,
Assa
--
Assa Yeroslaviz
L?tzenerstr. 15
51373 Leverkusen
On 11/2/05 7:47 AM, "Assa Yeroslaviz" <assa.yeroslaviz at="" uni-="" duesseldorf.de="">
wrote:
> Hi,
>
> Is there a way of extracting ONLY a list of the attributes of an
output file
> from the siggenes package?
>
> After doing a sam calculation:
>> A.out <- sam(AE0627999.data, AE0627999.cl,
> B=200,rand=123,gene.names=matrix_all_names[,2])
>
> I wanted than to look at the attributes of the file:
>> attributes(A.out)
>
> The List I've got is to long to be observed in my GUI window, so I
would like
> to
> know, if there is a possibility to only see the titles of the
attributes and
> not
> the whole list.
I'm not sure exactly what you want, but have you looked at:
help(SAM-class)
This is the object returned by SAM.
Sean
Assa Yeroslaviz wrote:
> Hi,
>
> Is there a way of extracting ONLY a list of the attributes of an
output file
> from the siggenes package?
>
> After doing a sam calculation:
>
>>A.out <- sam(AE0627999.data, AE0627999.cl,
>
> B=200,rand=123,gene.names=matrix_all_names[,2])
>
> I wanted than to look at the attributes of the file:
>
>>attributes(A.out)
Try
names(attributes(A.out))
Best,
Jim
>
>
> The List I've got is to long to be observed in my GUI window, so I
would like to
> know, if there is a possibility to only see the titles of the
attributes and not
> the whole list.
>
> THX,
>
> Assa
>
> --
> Assa Yeroslaviz
> L?tzenerstr. 15
> 51373 Leverkusen
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Hi there!
My aim was to get about 100 called genes out of the sam analysis which
I
have achieved doing this:
>sam9 <- sam(filtered, cl, delta=0.9, rand=2)
the delta of 0.9. gives me 120 Called genes:
>sam9
SAM Analysis for the Two-Class Unpaired Case Assuming Unequal
Variances
Delta p0 False Called FDR
0.900 0.570 8.920 120.000 0.042
and I now want to get all the Called genes to perform further anaylsis
(heatmap and so on). how can I do that?
I?ve tried several things like:
called <- sam9$Called
but with no success.
Thanks to everyone!
cheers,
gregor
