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Question: Help on beadarray
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gravatar for Haiming Chen
10.6 years ago by
Haiming Chen10
Haiming Chen10 wrote:
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 --------------------------------- ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink modified 10.6 years ago by Matt Ritchie460 • written 10.6 years ago by Haiming Chen10
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gravatar for Matt Ritchie
10.6 years ago by
Matt Ritchie460
Matt Ritchie460 wrote:
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 > ---------------------------------
ADD COMMENTlink written 10.6 years ago by Matt Ritchie460
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gravatar for Matt Ritchie
10.6 years ago by
Matt Ritchie460
Matt Ritchie460 wrote:
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
ADD COMMENTlink written 10.6 years ago by Matt Ritchie460
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