Hi Daniela.
That's strange. And no, these files do not need to be in a particular
directory (In fact, this error is completely independent of the
aroma.affmetrix package). The error you get suggests the file is empty.
When you say it "seems to be fine", what does that mean? Alternatively,
what does this give:
file.info("MoGene-1_0-st-v1.probe.tab")
This should be a decent sized file. The ZIP file that you get from
Affymetrix is 23MB, so unzipped it will be a lot larger.
Cheers,
Mark
> So far I have managed to nearly run everything of the script.
> I do though have issues in loading the probe sequences.
> Do the files need to be stored in a particular folder? For now I have
> it in ./annotationData/chipTypes/ as I have seen someone else in this
> forum doing it like this.
> What else could the reason be?
>
>> probetab<-read.table("MoGene-1_0-st-v1.probe.tab", sep="\t",header=TRUE,
>> comment.char="",stringsAsFactors=FALSE)
> Error in read.table("MoGene-1_0-st-v1.probe.tab", sep = "\t", header =
> TRUE, :
> no lines available in input
>
> I double checked the file I downloaded from Affy and it seems to be
> fine!
> Thx,
> Daniela
>
> On Mar 16, 4:56 pm, Mark Robinson <mrobin...@wehi.edu.au> wrote:
>> Hi Daniela.
>>
>> Those files are available from Affymetrix.
>>
>> For example,
>> see:http://www.affymetrix.com/estore/browse/products.jsp?productId=131453...
>>
>> HuGene-1_0-st-v1 Transcript Cluster Annotations, CSV, Release 30 (18
>> MB 11/09/09)
>> HuGene-1_0-st-v1 Probe Sequences, tabular format (22 MB 07/13/07)
>>
>> (there are different versions of the annotation files available)
>>
>> Cheers,
>> Mark
>>
>> On 13-Mar-10, at 8:12 AM, dkny169 wrote:
>>
>>
>>
>> > Hello,
>> > I am working on the sup3.R script (FIRMAGene).
>>
>> > I was wondering what kind of files these are: HuGene-1_0-st-
>> > v1.na25.hg18.transcript.csv and HuGene-1_0-st-v1.probe.tab?
>> > What is in these files?
>> > What am I supposed to load here into FIRMAGene?
>>
>> > Thanks a lot!
>>
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest version of the package, 2) to report the output of
>> > sessionInfo() and traceback(), and 3) to post a complete code example.
>>
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>>
>> ------------------------------
>> Mark Robinson, PhD (Melb)
>> Epigenetics Laboratory, Garvan
>> Bioinformatics Division, WEHI
>> e: m.robin...@garvan.org.au
>> e: mrobin...@wehi.edu.au
>> p: +61 (0)3 9345 2628
>> f: +61 (0)3 9347 0852
>> ------------------------------
>>
>> ______________________________________________________________________
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo()
> and traceback(), and 3) to post a complete code example.
>
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______________________________________________________________________
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You must not disclose, forward, print or use it without the permission of the
sender.
______________________________________________________________________
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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