Hi,
thanks for sending me an example CEL file offline. I've managed to
reproduce it. I've also made the code more robust against CEL files
with DAT header missing the chip type label. Update
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
and I think you can also analyze those problematic CEL files.
Hope this solved your problem
Henrik
On Sat, Aug 27, 2011 at 5:22 PM, Henrik Bengtsson
<henrik.bengts...@aroma-project.org> wrote:
> Hi,
>
> seeing these error messages, my best guess is that those CEL files
> with DAT headers containing only ".1sq" instead of the expected
> "GenomeWideSNP_6.1sq" are somehow corrupt and not real GenomeWideSNP_6
> CEL files. To be sure I need to study such a file. Would you mind
> making one of the ".1sq" CEL files available (ftp, website, ...) and
> I'll have a look at it.
>
> /Henrik
>
> On Fri, Aug 26, 2011 at 8:52 AM, Irina Ostrovnaya <rishe...@gmail.com> wrote:
>> Hi,
>> I'm encountering two errors:
>> 1) error happens with:
>> cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
>> print(cs)
>> Error in if (hasTimestamp) { : argument is of length zero
>>
>> It seems that samples that go through have:
>> getHeader(getFile(cs, 1))$datheader
>> [1] "[0..65534] D1_GenomeWideSNP_6:CLS=20508RWS=20508XIN=0 YIN=0
>> VE=0 0 12/10/10 12:05:43 50205130 M10 \024 \024
>> GenomeWideSNP_6.1sq \024 \024 \024 \024 \024 570 \024 25565.199219
>> \024 3.500000 \024 0.7000 \024 3"
>>
>> And samples that don't go through have something like:
>> getHeader(getFile(cs, 5))$datheader
>> [1] "[2..65534]
>> D2_plus_D1785_GenomeWideSNP_6:CLS=20491RWS=20491XIN=0 YIN=0
>> VE=0 0 12/09/10 01:52:21 50205130 M10 \024 \024 .1sq
>> \024 \024 \024 \024 \024 570 \024 25556.708984 \024 3.500000 \024
>> 0.7000 \024 3"
>>
>>
>> If I get rid of samples that have .1sq instead of GenomeWideSNP_6.1sq,
>> everything works
>>
[snip]
>>
>> sessionInfo()
>> R version 2.13.1 (2011-07-08)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices datasets utils methods base
>>
>> other attached packages:
>> [1] ACNE_0.4.3 MASS_7.3-13
>> aroma.affymetrix_2.1.6
>> [4] affxparser_1.24.0 aroma.apd_0.2.0 R.huge_0.3.0
>> [7] aroma.core_2.1.4 aroma.light_1.20.0 matrixStats_0.2.2
>> [10] R.rsp_0.6.2 R.cache_0.4.3 R.filesets_1.1.0
>> [13] digest_0.5.0 R.utils_1.7.8 R.oo_1.8.1
>> [16] R.methodsS3_1.2.1
>>
>>
>> Any recommendations?
>> Thanks!
>>
>> --
>> 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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>>
>
--
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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