[BioC] problem reading GenePix files with .XLS extension

[michael watson (IAH-C)]

Can you tell me if these are real Excel files or just text files with a
.xls extension? 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Srinivas
Iyyer
Sent: 29 September 2005 00:00
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] problem reading GenePix files with .XLS extension

Hello:


I am a fist time trying to analyze cdna data and right at the first step
i was bombed.  can any one please help me:


>library(Biobase)
>library(marray)
>samples = read.phenoData("phenodata.txt",header=TRUE,
as.is = TRUE)
> files = samples$fileName

spree of errors starts here:

## the .XLS files are downloaded from Garber_lung data. 
## software used in GenePix
## path : I am using windows based R so changed the ## directory to
where all my .XLS files area locatd

> mdata = read.GenePix(files, path=".")
Error in if (skip > 0) readLines(file, skip) : 
        missing value where TRUE/FALSE needed


>mdata = read.GenePix(files, ext = 'xls')
Error in if (skip > 0) readLines(file, skip) : 
        missing value where TRUE/FALSE needed


> mdata = read.marrayRaw(files,ext = "xls")
Error in if (is.na(pattern)) { : argument is of length zero

> nmdata = read.marrayRaw(nfs, ext="xls")
Error in if (is.na(pattern)) { : argument is of length zero
> nmdata = read.marrayRaw(nfs, ext="xls", skip = 22)
Reading ...  ./shu058.248-97_LCLC.xls
Error in read.table(f, skip = skip2, header = TRUE, sep = sep, quote =
quote,  : 
        unused argument(s) (ext ...)


How do I read these XLS files and retain all the
inforamtion. 

can any one please give R commands till I get to
normalization procedure. 

Thank you

srini

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/bioconductor