Dear Dr.:
I am interested in using the R package BeadArray to analyze my
Illumina
Beadchip expression data. There is an error message when typing the
command
"readIllumina(texType=".csv")":
Error in strtrim(x, width) : invalid 'width' argument
Please if you ccould provide assistance. Many thanks!
/// Haiming
---------------------------------
Haiming Chen, M.D., M.Sc.
Department of Psychiatry
University of Michigan Med Sch
BSRB 5063
109 Zina Pitcher Pl.
Ann Arbor, MI 48109
---------------------------------
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Dear Haiming,
I think the problem is that the readIllumina() function is unable to
find
the raw .csv and/or .tif files that it needs. Try typing dir() at the
R
command prompt to see whether these files are available in the current
working directory. If they aren't, you'll need to change your working
directory (type ?setwd for more information on how to do this).
I have checked in a new version of readIllumina() into beadarray 1.5.1
that
gives a more meaningful error message when the raw files cannot be
found.
I hope this helps. Best wishes,
Matt
> Dear Dr.:
> I am interested in using the R package BeadArray to analyze my
Illumina
> Beadchip expression data. There is an error message when typing the
command
> "readIllumina(texType=".csv")":
>
> Error in strtrim(x, width) : invalid 'width' argument
>
> Please if you ccould provide assistance. Many thanks!
>
>
> /// Haiming
> ---------------------------------
> Haiming Chen, M.D., M.Sc.
>
> Department of Psychiatry
> University of Michigan Med Sch
> BSRB 5063
> 109 Zina Pitcher Pl.
> Ann Arbor, MI 48109
> ---------------------------------
Dear Haiming,
Changing the file extension isn't a good idea. In your case, the
argument
'textType' in readIllumina needs to be changed to ".txt" rather than
".csv"
as the raw data from the scanner is stored in tab delimited text
files. So
try
BLdata <- readIllumina(textType=".txt")
and take a look at the readIllumina help page (?readIllumina) to find
out
more about 'textType' and the other arguments in readIllumina.
Best wishes,
Matt
> Dear Matt;
> Thanks for replying my email re Beadarray. I did the way that you
suggested,
> also renamed the "*.txt" files (bead data, X-Y co-ord) to ".*csv",
however,
> another error message here:
>
>> BLdata <- readIllumina(textType=".csv")
> Found 8 arrays
> Error in order(dat1$ProbeID) : object "dat1" not found
>>
>
>
> what does "dat1" object mean? Is it an output from the scanner?
>
> Best,
>
> /// Haiming
