Question: attributes of SAM files
0
gravatar for Assa Yeroslaviz
14.1 years ago by
Assa Yeroslaviz100 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. THX, Assa -- Assa Yeroslaviz L?tzenerstr. 15 51373 Leverkusen
gui siggenes • 493 views
ADD COMMENTlink modified 14.1 years ago by James W. MacDonald52k • written 14.1 years ago by Assa Yeroslaviz100
Answer: attributes of SAM files
0
gravatar for Sean Davis
14.1 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 14.1 years ago by Sean Davis21k
Answer: attributes of SAM files
0
gravatar for James W. MacDonald
14.1 years ago by
United States
James W. MacDonald52k wrote:
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
ADD COMMENTlink written 14.1 years ago by James W. MacDonald52k
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
ADD REPLYlink written 14.1 years ago by Gregor Siegler50
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