[BioC] Nimblegen chip analysis

[Todd Richmond]

Hi Rene,

Since we've never made a design called "60merProbeSeqs", I suspect that you're working with a file that has been filtered somehow, possibly to include only the experimental probes. If you check the header line of the .xys file, there is a tag/value pair with the name of the design used to create the file. That's the one you need to use makePDpackage.

Todd

--
Todd Richmond
NimbleGen Systems, Inc.
Manager of Research Informatics
One Science Court
Madison, WI 53711
1-608-218-7600


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of Rene Dreos (JIC)
> Sent: Wednesday, July 11, 2007 3:43 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Nimblegen chip analysis
>
> Dear list,
> I am trying to build a Nimblegen platform package using
> makePlatformDesign. Nimblagen technical support provide me the .xys file
> for this platform but when I try to build the package the software give
> me this error:
>
> > makePDpackage("60merProbeSeqs.ndf", "1140102_532.xys", manufacturer =
> > "nimblegen")
> nimblegen expression
> The package will be called pd.60merprobeseqs Reading 60merProbeSeqs.txt
> Assuming a simple design (NOT multiple-wells).
> Error in data.frame(X = ndfdata$X, Y = ndfdata$Y, feature_set_name =
> ndfdata$SEQ_ID,  :
>         arguments imply differing number of rows: 0, 392247 In addition:
> Warning messages:
> 1: no non-missing arguments to max; returning -Inf in: max(ndfdata$X)
> 2: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y)
> 3: no non-missing arguments to max; returning -Inf in: max(ndfdata$Y)
> >
>
> I check the number of lines in the .ndf, it is 372776 but the number of
> lines in the .xys is 392247.
> How can I solve this problem?
> Regards
> Rene'
>
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