[BioC] Bioconductor Digest, Vol 87, Issue 10

[Saroj K Mohapatra]

Hi Avinash:

I have never used hopach. But as the vignette suggests, you could get 
the information from the documentation for golub data.

 > require(hopach)
 > ?golub

gives me the details of golub data:

-----------------------
golub package:hopach R Documentation

Gene expression dataset from Golub et al. (1999)

Description:

Gene expression data (3051 genes and 38 tumor mRNA samples) from
the leukemia microarray study of Golub et al. (1999).
Pre-processing was done as described in Dudoit et al. (2002). The
R code for pre-processing is available in the file golub.R in the
docs directory.

Usage:

data(golub)

Value:

golub: matrix of gene expression levels for the 38 tumor mRNA
samples, rows correspond to genes (3051 genes) and columns to
mRNA samples.

golub.cl: numeric vector indicating the tumor class, 27 acute
lymphoblastic leukemia (ALL) cases (code 0) and 11 acute
myeloid leukemia (AML) cases (code 1).

golub.gnames: a matrix containing the names of the 3051 genes for the
expression matrix ‘golub’. The three columns correspond to
the gene ‘index’, ‘ID’, and ‘Name’, respectively.
----------------------------

To make your data similar to this, the following 3 objects need to be 
created:
yourdata: a numerical matrix, rows for genes, columns for samples
yourclassvec: a vector with same length as number of columns, made up of 
0s and 1s
yourgeneann: a matrix with number of rows same as yourdata, 3 columns

I hope then it should be straight forward to implement hopach.

Hope that helps. Best wishes,

Saroj

avinash gupta wrote:
> sir,
>         i work on microarry analysis using R and bioconductor . i had read
> the data from array express creat the object and normalize it .now i want to
> do clustering by HOPACH method .In the manual of hopach method  first  load
> the necessary packages (hopach) , in second step load the data set ,they use
> the golub data ,i don't understand it that how it prepared and what type of
> data is stored in this data set and in my project what type of object or
> data i use  in the place of golub like simple object or after normalization
> object. . Please mail me coding or manual of making of golub dataset or
> manual  for making any data set from any object data .
>