Hi.
On Fri, Mar 11, 2011 at 3:01 AM, Ajanthah Sangaralingam
<a.sangaralin...@qmul.ac.uk> wrote:
> Hi,
>
> Thank you the append function now works - I have installed the patch, but I
> am having some difficulty with the setFullName function which worked okay in
> the previous version does anyone know if there is a different way to do this
> in the updated version?
>
>>csCancer <- AffymetrixCelSet$byName("project1",cdf=cdf)
>>csNormals <- AffymetrixCelSet$byName("JPT",cdf=cdf)
>>csR <- append(csCancer,csNormals);
>>setFullName(csR,paste(csCancer,csNormals,sep=""));
That has most likely never worked as you intended. It may have
silently accepted it, but never worked correctly. The most recent
version of R.filesets does more validation and catches the error. The
error message is correct though possibly obscure. If you split it up
you code in two lines:
newFullName <- paste(csCancer, csNormals, sep="");
setFullName(csR,newFullName);
and look at what print(newFullName) gives, you'll understand. It is
not a single character string!
You probably want:
newFullName <- paste(getFullName(csCancer), getFullName(csNormals), sep="");
>
>>cSR
>
> csR
> Error in list(`print(NA)` = <environment>, `print.Object(NA)` =
> <environment>, :
>
> [2011-03-11 10:54:29] Exception: Failed to translate full names. The
> translator is erroneous, because it drops/adds some names (passed 1 names
> but got 11 names).
> at throw(Exception(...))
> at throw.default(sprintf("Failed to translate full names. The translator
> is er
> at throw(sprintf("Failed to translate full names. The translator is
> erroneous,
> at translateFullName.FullNameInterface(this, fullname)
> at translateFullName(this, fullname)
> at getFullName.FullNameInterface(this, ...)
> at getFullName(this, ...)
> at getName.FullNameInterface(this)
> at getName(this)
> at sprintf("Name: %s", getName(this))
> at as.character.AffymetrixCelSet(x)
> at as.character(x)
> at print(as.character(x))
> at print.Object(NA)
> at print(NA)
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-unknown-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] sfit_0.1.9 aroma.affymetrix_2.0.0 aroma.apd_0.1.8
> [4] affxparser_1.22.1 R.huge_0.2.2 aroma.core_2.0.0
> [7] aroma.light_1.18.3 matrixStats_0.2.2 R.rsp_0.4.5
> [10] R.cache_0.4.0 R.filesets_0.9.5 digest_0.4.2
> [13] R.utils_1.6.5 R.oo_1.7.5 R.methodsS3_1.2.1
>
>
>
>
>
> On 11/03/2011 04:20, "Henrik Bengtsson" <henrik.bengts...@aroma-project.org>
> wrote:
>
>> Hi,
>>
>> I've located the problem and fixed it. I've made a patch available
>> that you can use until the next package release is available. To
>> install the patch, just do:
>>
>> source("http://aroma-project.org/hbLite.R";);
>> hbInstall("aroma.affymetrix");
>>
>> /Henrik
>>
>> On Thu, Mar 10, 2011 at 10:01 AM, Henrik Bengtsson
>> <henrik.bengts...@aroma-project.org> wrote:
>>> Thanks for reporting this. I'll fix it asap. In the meanwhile, here
>>> is an ad hoc patch:
>>>
>>> appendT <- function(cs1, cs2, ...) {
>>> files <- append(as.list(cs1), as.list(cs2));
>>> newInstance(cs1, files);
>>> }
>>>
>>> Then
>>>
>>> csR <- appendT(csCancer, csNormals);
>>>
>>> should work.
>>>
>>> /Henrik
>>>
>>>
>>> On Thu, Mar 10, 2011 at 9:52 AM, Ajanthah Sangaralingam
>>> <a.sangaralin...@qmul.ac.uk> wrote:
>>>> Dear All,
>>>>
>>>> I have recently upgraded to the latest version of aroma.affymetrix and am
>>>> experiencing problems running the code below
>>>>
>>>>> csCancer <- AffymetrixCelSet$byName(³project1²,cdf=cdf)
>>>>> csNormals <- AffymetrixCelSet$byName(³JPT²,cdf=cdf)
>>>>> csR <- append(csCancer, csNormals);
>>>>
>>>> project1 and JPT are datasets in the rawData directory.
>>>>
>>>> I get the following error:
>>>>
>>>> Error in base::append(this$files, files, ...) :
>>>> unused argument(s) (other = NA)
>>>>
>>>>
>>>> This code ran okay in the previous version of aroma and I wondered if the
>>>> append function worked differently in the new version of aroma?
>>>>
>>>>
>>>> sessionInfo()
>>>> R version 2.12.2 (2011-02-25)
>>>> Platform: x86_64-unknown-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] sfit_0.1.9 aroma.affymetrix_2.0.0 aroma.apd_0.1.8
>>>> [4] affxparser_1.22.1 R.huge_0.2.2 aroma.core_2.0.0
>>>> [7] aroma.light_1.18.3 matrixStats_0.2.2 R.rsp_0.4.2
>>>> [10] R.cache_0.4.0 R.filesets_0.9.2 digest_0.4.2
>>>> [13] R.utils_1.6.3 R.oo_1.7.5 R.methodsS3_1.2.1
>>>>
>>>> Many thanks
>>>>
>>>> Ajanthah
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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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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>>>>
>>>
>
> --
> 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.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
