[BioC] data() function problem

[ZRG (Zeren Gao)]

Hi there,
Here is the detail of my problem. 
1) I am try to find genes with expression level correlates to a specified gene. 
2) Therefore, I try to fun genefinder, whcih will find genes 'close' to specified genes, I am not sure what close meant here, is the absolute expression level close or have correlation. I assume is the later.
3) I try to run it as describe in the example. following is my command line
with window verion.
>library(genefilter)
>data(C://.......file.txt)
it become "load...." automatically, instead of read.table.
Therefore I read in the data file
>file <- read.table(C://....file.txt, header=TRUE)
>igenes <-c(19202)
>closeg <- genefinder(file, igenes, 10, method= "euc", scale = "none")
I got an error message:
Error in genefinder(file, igenes, 10, method = "euc", scale = "none") : 
No direct or inherited method for function "genefinder" for this call

So I don't know what is going on. 
1)I have run the example with supplied data 'eset', works fine. 
2)I am not sure if data() did anything to the file make genefinder works 
3)I am not sure why data() refuse to read file.txt

more help needed. 

Thanks a lot.

Zeren Gao 

-----Original Message-----
From: John Zhang [mailto:jzhang at jimmy.harvard.edu]
Sent: Thursday, May 08, 2003 7:33 AM
To: ZRG (Zeren Gao); bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] data() function problem




>I try to run example of genefilter and the data() has following error 
>Error: bad restore file magic number (file may be corrupted)-- no data loaded

Can you be more specific on what example you were running on what data set?

>it works fine with sample data set 'eset', therefore, it clearly needs to some 
how change my data format. 
>My data format is 
>probe		exp1		exp2	...
>1037_at		23		34	...

Were you using data() to read your own data set? data() works like this:

        1.  files ending `.R' or `.r' are `source()'d in, with the R
            working directory changed temporarily to the directory
            containing the respective file.

        2.  files ending `.RData' or `.rda' are `load()'ed.

        3.  files ending `.tab', `.txt' or `.TXT' are read using
           `read.table(..., header = TRUE)', and hence result in a data
           frame.

        4.  files ending `.csv' or `.CSV' are read using
           `read.table(..., header = TRUE, sep = ";")', and also result
           in a data frame.

Do you have the correct extension?

>
>any comments?
>Thanks.
>Zeren Gao
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084