Hi There, 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 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 ... any comments? Thanks. Zeren Gao

>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@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

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@jimmy.harvard.edu] Sent: Thursday, May 08, 2003 7:33 AM To: ZRG (Zeren Gao); bioconductor@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@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

>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@jimmy.harvard.edu] >Sent: Thursday, May 08, 2003 7:33 AM >To: ZRG (Zeren Gao); bioconductor@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@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@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

>> 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@jimmy.harvard.edu] >Sent: Friday, May 09, 2003 5:37 AM >To: ZRG (Zeren Gao); bioconductor@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@jimmy.harvard.edu] >>Sent: Thursday, May 08, 2003 7:33 AM >>To: ZRG (Zeren Gao); bioconductor@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@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@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

Hi there, This time I used "sep" in my read.table command, still get the same resutls as showing below: > test <- read.table("C:/My Download Files/microarray/PGA-HCL/PGA- HCL_UA_dat_r.txt", header = TRUE, sep = "\t") > 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@jimmy.harvard.edu] Sent: Friday, May 09, 2003 5:37 AM To: ZRG (Zeren Gao); bioconductor@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@jimmy.harvard.edu] >Sent: Thursday, May 08, 2003 7:33 AM >To: ZRG (Zeren Gao); bioconductor@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@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@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