[BioC] LumiR

[Pan Du]

Hi Giovanni,

We have never tested the BeadStudio output of version 1.5.1.3. They might
change the output format again. You know they made quite a few changes from
version 1.0 to 1.3. Can you send me part of the text file, like top 100 rows
to me? Thanks.


Pan


On 8/16/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 7
> Date: Wed, 15 Aug 2007 08:04:05 -0700
> From: "Giovanni Coppola" <gcoppola at ucla.edu>
> Subject: Re: [BioC] LumiR
> To: bioconductor at stat.math.ethz.ch
> Message-ID:
> <f459aed80708150804m71ee2c8dkb822b5bd564d7409 at mail.gmail.com>
> Content-Type: text/plain
> 
> Hello everybody,
> I am trying to read in a .csv BeadStudio output (version 1.5.1.3) and I get
> the following error:
>> lumiData<- lumiR("mydata.csv")
> Error in var(x, na.rm = na.rm) : 'x' is empty
> In addition: Warning messages:
> 1: NAs introduced by coercion in: as.double.default(exprs)
> 2: NAs introduced by coercion in: as.double.default(se.exprs)
> 3: NAs introduced by coercion in: as.double.default(detection)
> 4: NAs introduced by coercion in: as.double.default(beadNum)
> 5: no non-missing arguments to max; returning -Inf in: max(exprs, na.rm =
> TRUE)
> 
> 
> The error happens a while after the command is issued, suggesting that the
> file is read in first (empty lines at the bottom?). I tried also setting
> na.rm=F, without success.
> Any suggestions?
> Thanks
> Giovanni