[BioC] data() function problem

[John Zhang]

>> test <- read.table("C:/My Download 
Files/microarray/PGA-HCL/PGA-HCL_UA_dat_r.txt", header = TRUE, sep = "\t")

Check to see if test was read in correctly (e.g. with correct sep). 
genefinder expects test to be a numeric matrix with columns for experiments and 
rows for genes.

You may also what to do a debug on genefinder to see where it fails.

>> igenes <- c(19202)
>> closeg <- genefinder(test, igenes, 10, method = "euc", scale = "none")
>Error in genefinder(test, igenes, 10, method = "euc", scale = "none") : 
>        No direct or inherited method for function "genefinder" for this call
>
>Any suggestion why is this happening? what is direct or inherited method here? 
>thanks a lot for helping. 
>Zeren gao
> 
>
>-----Original Message-----
>From: John Zhang [mailto:jzhang at jimmy.harvard.edu]
>Sent: Friday, May 09, 2003 5:37 AM
>To: ZRG (Zeren Gao); bioconductor at stat.math.ethz.ch
>Subject: RE: [BioC] data() function problem
>
>
>
>>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)
>
>What is the separator for the file? The default for read.table is "" but your 
>file seems to have a tab ("\t") separator. Try file <- 
>read.table(C://....file.txt, header=TRUE, sep = "\t")
>
>>>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
>
>genefinder expects file to be a matrix, which may not be true if file is not 
>read correctly.
>
>
>>
>>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
>>>
>>>_______________________________________________
>>>Bioconductor mailing list
>>>Bioconductor at stat.math.ethz.ch
>>>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>>
>>Jianhua Zhang
>>Department of Biostatistics
>>Dana-Farber Cancer Institute
>>44 Binney Street
>>Boston, MA 02115-6084
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
>Jianhua Zhang
>Department of Biostatistics
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084
>

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084