Dear List,
I'm new to microarray analysis, so go easy. When I try to import some
methylation data using lumiR, I receive the following error:
> meth<-lumiR("~/desktop/meth_sample.txt")
Error in gregexpr("\t", dataLine1) : invalid 'text' argument
If I specify "sep":
> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
subscript out of bounds
Does anyone know what might be causing the problem? Can lumiR handle
this type of data where headers from BeadStudio are "..._Beta" instead
of "..._Signal", etc
Thank you,
Paul Sanfilippo
Hi Paul
Please provide more detailed information, or else we cannot help you.
For example, please send me the returns of sessionInfo() and also the
top
twenty lines of your data. I want to know whether it is because you
are
using outdated packages or data in the wrong format.
Thanks!
Pan
On 1/16/10 5:24 PM, "gilbert feng" <g-feng at="" northwestern.edu=""> wrote:
> From: Paul Sanfilippo <prseye at="" gmail.com="">
> Date: Sun, 17 Jan 2010 10:16:41 +1100
> To: <bioconductor at="" stat.math.ethz.ch="">
> Subject: [BioC] lumiR error
>
> Dear List,
>
> I'm new to microarray analysis, so go easy. When I try to import
some
> methylation data using lumiR, I receive the following error:
>
>> meth<-lumiR("~/desktop/meth_sample.txt")
> Error in gregexpr("\t", dataLine1) : invalid 'text' argument
>
> If I specify "sep":
>
>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
> subscript out of bounds
>
> Does anyone know what might be causing the problem? Can lumiR handle
> this type of data where headers from BeadStudio are "..._Beta"
instead
> of "..._Signal", etc
>
> Thank you,
>
> Paul Sanfilippo
--
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL 60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan (at) northwestern.edu
Hi Paul
Your data is Illumina Methylation data, not expression data. You need
to use
³methylumi² package to preprocess the data.
Actually, Sean Davis also told me this this morning.
Pan
On 1/18/10 4:43 PM, "Paul Sanfilippo" <prseye@gmail.com> wrote:
> Hi Pan,
>
> I'm thinking the data is in the wrong format, but am keen to know if
there's a
> way around this (eg remapping column headers)
>
>> > sessionInfo()
> R version 2.10.1 Patched (2009-12-29 r50852)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C/C/en_US/C/C/C
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets
methods
> [8] base
>
> other attached packages:
> [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1
> [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1
> [7] affy_1.24.2 annotate_1.24.1 AnnotationDbi_1.8.1
> [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2
> [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8
> [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2
> [19] rJava_0.8-1
>
> loaded via a namespace (and not attached):
> [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26
nlme_3.1-96
> [5] tools_2.10.1 xtable_1.5-6
>> >
>
> This is the data format that I have (I've just included the first
subject
> columns (in yellow))
>
>
>
> Many thanks.
>
> Regards,
>
> Paul
>
> Pan Du wrote:
>>
>> Hi Paul
>>
>> Please provide more detailed information, or else we cannot help
you.
>> For example, please send me the returns of sessionInfo() and also
the top
>> twenty lines of your data. I want to know whether it is because you
are
>> using outdated packages or data in the wrong format.
>> Thanks!
>>
>> Pan
>>
>>
>> On 1/16/10 5:24 PM, "gilbert feng" <g-feng@northwestern.edu>
>> <mailto:g-feng@northwestern.edu> wrote:
>>
>>
>>
>>>
>>> From: Paul Sanfilippo <prseye@gmail.com> <mailto:prseye@gmail.com>
>>> Date: Sun, 17 Jan 2010 10:16:41 +1100
>>> To: <bioconductor@stat.math.ethz.ch>
<mailto:bioconductor@stat.math.ethz.ch>
>>> Subject: [BioC] lumiR error
>>>
>>> Dear List,
>>>
>>> I'm new to microarray analysis, so go easy. When I try to import
some
>>> methylation data using lumiR, I receive the following error:
>>>
>>>
>>>
>>>>
>>>> meth<-lumiR("~/desktop/meth_sample.txt")
>>>>
>>>>
>>>
>>> Error in gregexpr("\t", dataLine1) : invalid 'text' argument
>>>
>>> If I specify "sep":
>>>
>>>
>>>
>>>>
>>>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
>>>>
>>>>
>>>
>>> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
>>> subscript out of bounds
>>>
>>> Does anyone know what might be causing the problem? Can lumiR
handle
>>> this type of data where headers from BeadStudio are "..._Beta"
instead
>>> of "..._Signal", etc
>>>
>>> Thank you,
>>>
>>> Paul Sanfilippo
>>>
>>>
>>
>>
[[alternative HTML version deleted]]
Ok thanks.
I thought I'd have a go with other packages as I hit a roadblock with
methylumi in trying a normalisation.
Thanks again for your help.
Paul
Pan Du wrote:
> Hi Paul
>
> Your data is Illumina Methylation data, not expression data. You
need
> to use "methylumi" package to preprocess the data.
> Actually, Sean Davis also told me this this morning.
>
>
> Pan
>
>
> On 1/18/10 4:43 PM, "Paul Sanfilippo" <prseye@gmail.com> wrote:
>
> Hi Pan,
>
> I'm thinking the data is in the wrong format, but am keen to
know
> if there's a way around this (eg remapping column headers)
>
> > sessionInfo()
> R version 2.10.1 Patched (2009-12-29 r50852)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C/C/en_US/C/C/C
>
> attached base packages:
> [1] grid stats graphics grDevices utils datasets
> methods
> [8] base
>
> other attached packages:
> [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1
> [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1
> [7] affy_1.24.2 annotate_1.24.1
AnnotationDbi_1.8.1
> [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2
> [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8
> [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2
> [19] rJava_0.8-1
>
> loaded via a namespace (and not attached):
> [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26
> nlme_3.1-96
> [5] tools_2.10.1 xtable_1.5-6
> >
>
> This is the data format that I have (I've just included the
first
> subject columns (in yellow))
>
>
>
> Many thanks.
>
> Regards,
>
> Paul
>
> Pan Du wrote:
>
>
> Hi Paul
>
> Please provide more detailed information, or else we cannot
> help you.
> For example, please send me the returns of sessionInfo() and
> also the top
> twenty lines of your data. I want to know whether it is
> because you are
> using outdated packages or data in the wrong format.
> Thanks!
>
> Pan
>
>
> On 1/16/10 5:24 PM, "gilbert feng" <g-feng@northwestern.edu>
> <mailto:g-feng@northwestern.edu> wrote:
>
>
>
>
> From: Paul Sanfilippo <prseye@gmail.com>
> <mailto:prseye@gmail.com>
> Date: Sun, 17 Jan 2010 10:16:41 +1100
> To: <bioconductor@stat.math.ethz.ch>
> <mailto:bioconductor@stat.math.ethz.ch>
> Subject: [BioC] lumiR error
>
> Dear List,
>
> I'm new to microarray analysis, so go easy. When I try
to
> import some
> methylation data using lumiR, I receive the following
error:
>
>
>
>
> meth<-lumiR("~/desktop/meth_sample.txt")
>
>
>
> Error in gregexpr("\t", dataLine1) : invalid 'text'
argument
>
> If I specify "sep":
>
>
>
>
> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
>
>
>
> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
> subscript out of bounds
>
> Does anyone know what might be causing the problem? Can
> lumiR handle
> this type of data where headers from BeadStudio are
> "..._Beta" instead
> of "..._Signal", etc
>
> Thank you,
>
> Paul Sanfilippo
>
>
>
>
[[alternative HTML version deleted]]
No worries Sean.
No pressure - I appreciate any help I can get.
Regards,
Paul
Sean Davis wrote:
> On Mon, Jan 18, 2010 at 5:55 PM, Paul Sanfilippo<prseye@gmail.com>
wrote:
>
>> Ok thanks.
>>
>> I thought I'd have a go with other packages as I hit a roadblock
with
>> methylumi in trying a normalisation.
>>
>
> Sorry, Paul. I have been busy and haven't gotten to looking at your
> problem. I hope to get to that in the next day or so.
>
> Sean
>
>
>
>> Pan Du wrote:
>>
>>> Hi Paul
>>>
>>> Your data is Illumina Methylation data, not expression data. You
need
>>> to use "methylumi" package to preprocess the data.
>>> Actually, Sean Davis also told me this this morning.
>>>
>>>
>>> Pan
>>>
>>>
>>> On 1/18/10 4:43 PM, "Paul Sanfilippo"<prseye@gmail.com> wrote:
>>>
>>> Hi Pan,
>>>
>>> I'm thinking the data is in the wrong format, but am keen to
know
>>> if there's a way around this (eg remapping column headers)
>>>
>>> > sessionInfo()
>>> R version 2.10.1 Patched (2009-12-29 r50852)
>>> x86_64-apple-darwin9.8.0
>>>
>>> locale:
>>> [1] C/C/en_US/C/C/C
>>>
>>> attached base packages:
>>> [1] grid stats graphics grDevices utils
datasets
>>> methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] lumi_1.12.2 MASS_7.3-4 RSQLite_0.8-1
>>> [4] DBI_0.2-5 preprocessCore_1.8.0 mgcv_1.6-1
>>> [7] affy_1.24.2 annotate_1.24.1
AnnotationDbi_1.8.1
>>> [10] Biobase_2.6.1 ggplot2_0.8.5 digest_0.4.2
>>> [13] reshape_0.8.3 plyr_0.1.9 proto_0.3-8
>>> [16] JGR_1.7-0 iplots_1.1-3 JavaGD_0.5-2
>>> [19] rJava_0.8-1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Matrix_0.999375-33 affyio_1.14.0 lattice_0.17-26
>>> nlme_3.1-96
>>> [5] tools_2.10.1 xtable_1.5-6
>>> >
>>>
>>> This is the data format that I have (I've just included the
first
>>> subject columns (in yellow))
>>>
>>>
>>>
>>> Many thanks.
>>>
>>> Regards,
>>>
>>> Paul
>>>
>>> Pan Du wrote:
>>>
>>>
>>> Hi Paul
>>>
>>> Please provide more detailed information, or else we
cannot
>>> help you.
>>> For example, please send me the returns of sessionInfo()
and
>>> also the top
>>> twenty lines of your data. I want to know whether it is
>>> because you are
>>> using outdated packages or data in the wrong format.
>>> Thanks!
>>>
>>> Pan
>>>
>>>
>>> On 1/16/10 5:24 PM, "gilbert
feng"<g-feng@northwestern.edu>
>>> <mailto:g-feng@northwestern.edu> wrote:
>>>
>>>
>>>
>>>
>>> From: Paul Sanfilippo<prseye@gmail.com>
>>> <mailto:prseye@gmail.com>
>>> Date: Sun, 17 Jan 2010 10:16:41 +1100
>>> To:<bioconductor@stat.math.ethz.ch>
>>> <mailto:bioconductor@stat.math.ethz.ch>
>>> Subject: [BioC] lumiR error
>>>
>>> Dear List,
>>>
>>> I'm new to microarray analysis, so go easy. When I
try to
>>> import some
>>> methylation data using lumiR, I receive the following
error:
>>>
>>>
>>>
>>>
>>> meth<-lumiR("~/desktop/meth_sample.txt")
>>>
>>>
>>>
>>> Error in gregexpr("\t", dataLine1) : invalid 'text'
argument
>>>
>>> If I specify "sep":
>>>
>>>
>>>
>>>
>>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
>>>
>>>
>>>
>>> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]]
:
>>> subscript out of bounds
>>>
>>> Does anyone know what might be causing the problem?
Can
>>> lumiR handle
>>> this type of data where headers from BeadStudio are
>>> "..._Beta" instead
>>> of "..._Signal", etc
>>>
>>> Thank you,
>>>
>>> Paul Sanfilippo
>>>
>>>
>>>
>>>
>>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>>
>>
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