Hi,
I am trying to annotate the Nimblegen 385k mm8 refseq promoter chip
and the following is what I have been using:
> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS",
"2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen",
type="expression", genomebuild = "mm8")
nimblegen expression
The package will be called pd.2006.07.18.mm8.refseq.promoter
Reading 2006-07-18_MM8_RefSeq_promoter.ndf
Assuming a simple design (NOT multiple-wells).
Correcting probe positions... Done.
Error in getClass(Class, where = topenv(parent.frame())) :
"platformDesign" is not a defined class
Could anybody help me out with this? Moreover, is there a way to
convert .pair files into .XYS files for nimblegen?
Thank so much,
Som.
_________________________________________________________________
Hotmail: Trusted email with powerful SPAM protection.
[[alternative HTML version deleted]]
On Mon, Mar 1, 2010 at 3:27 PM, somnath bandyopadhyay
<genome1976 at="" hotmail.com=""> wrote:
>
> Hi,
>
> I am trying to annotate the Nimblegen 385k mm8 ?refseq promoter chip
and the following is what I have been using:
>
>
>
>> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS",
"2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen",
type="expression", genomebuild = "mm8")
> nimblegen expression
> The package will be called pd.2006.07.18.mm8.refseq.promoter
> Reading 2006-07-18_MM8_RefSeq_promoter.ndf
> Assuming a simple design (NOT multiple-wells).
> Correcting probe positions... Done.
> Error in getClass(Class, where = topenv(parent.frame())) :
> ?"platformDesign" is not a defined class
>
>
>
> Could anybody help me out with this? Moreover, is there a way to
convert .pair files into .XYS files for nimblegen?
Hi, Somnath. It is always useful to include sessionInfo() output when
reporting errors. Without this information, it is difficult to
determine what the problem might be.
Sean
Sorry about that. I am including the sessionInfo here:
> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS",
"2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen",
type="expression", genomebuild = "mm8")
nimblegen expression
The package will be called pd.2006.07.18.mm8.refseq.promoter
Reading 2006-07-18_MM8_RefSeq_promoter.ndf
Assuming a simple design (NOT multiple-wells).
Correcting probe positions... Done.
Error in getClass(Class, where = topenv(parent.frame())) :
"platformDesign" is not a defined class
> sessionInfo()
R version 2.10.0 beta (2009-10-16 r50118)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] makePlatformDesign_1.10.0 affyio_1.13.5 biomaRt_2.2.0
Ringo_1.10.0 Matrix_0.999375-37 lattice_0.18-3
[7] limma_3.2.1 RColorBrewer_1.0-2
pdInfoBuilder_1.10.1 oligo_1.10.2
preprocessCore_1.7.9 oligoClasses_1.7.16
[13] affxparser_1.18.0 RSQLite_0.8-3 DBI_0.2-5
Biobase_2.5.8
loaded via a namespace (and not attached):
[1] annotate_1.23.4 AnnotationDbi_1.7.20 Biostrings_2.14.12
genefilter_1.25.10 IRanges_1.4.11 RCurl_1.3-1
splines_2.10.0 survival_2.35-8
[9] tools_2.10.0 XML_2.6-0 xtable_1.5-6
>
> Date: Mon, 1 Mar 2010 15:38:18 -0500
> Subject: Re: [BioC] makePDpackage
> From: seandavi@gmail.com
> To: genome1976@hotmail.com
> CC: bioconductor@stat.math.ethz.ch
>
> On Mon, Mar 1, 2010 at 3:27 PM, somnath bandyopadhyay
> <genome1976@hotmail.com> wrote:
> >
> > Hi,
> >
> > I am trying to annotate the Nimblegen 385k mm8 refseq promoter
chip and the following is what I have been using:
> >
> >
> >
> >> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS",
"2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen",
type="expression", genomebuild = "mm8")
> > nimblegen expression
> > The package will be called pd.2006.07.18.mm8.refseq.promoter
> > Reading 2006-07-18_MM8_RefSeq_promoter.ndf
> > Assuming a simple design (NOT multiple-wells).
> > Correcting probe positions... Done.
> > Error in getClass(Class, where = topenv(parent.frame())) :
> > "platformDesign" is not a defined class
> >
> >
> >
> > Could anybody help me out with this? Moreover, is there a way to
convert .pair files into .XYS files for nimblegen?
>
> Hi, Somnath. It is always useful to include sessionInfo() output
when
> reporting errors. Without this information, it is difficult to
> determine what the problem might be.
>
> Sean
_________________________________________________________________
Hotmail: Trusted email with Microsofts powerful SPAM protection.
[[alternative HTML version deleted]]
Hi Som,
use the pdInfoBuilder package instead.
About PAIR -> XYS... you need to create a text file with the following
columns (X/Y/SIGNAL/COUNT). It should be sorted by X and Y coordinates
and control probes should have NA in the SIGNAL column. All X/Y
coordinates should be included.
X Y SIGNAL COUNT
1 1 321.12 1
1 2 NA 1
1 3 123.34 1
.. .. .....
The XYS files can be generated directly from NimbleScan....
b
On Mon, Mar 1, 2010 at 8:27 PM, somnath bandyopadhyay
<genome1976 at="" hotmail.com=""> wrote:
>
> Hi,
>
> I am trying to annotate the Nimblegen 385k mm8 ?refseq promoter chip
and the following is what I have been using:
>
>
>
>> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS",
"2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen",
type="expression", genomebuild = "mm8")
> nimblegen expression
> The package will be called pd.2006.07.18.mm8.refseq.promoter
> Reading 2006-07-18_MM8_RefSeq_promoter.ndf
> Assuming a simple design (NOT multiple-wells).
> Correcting probe positions... Done.
> Error in getClass(Class, where = topenv(parent.frame())) :
> ?"platformDesign" is not a defined class
>
>
>
> Could anybody help me out with this? Moreover, is there a way to
convert .pair files into .XYS files for nimblegen?
>
>
>
> Thank so much,
>
> Som.
>
> _________________________________________________________________
> Hotmail: Trusted email with powerful SPAM protection.
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Dear Som,
I'm bringing this message back to the mailing list so it can be used
as
reference for others.
COUNT is the number of features... You don't need to worry about this,
just
make it 1.
Once you have the XYS files, you should use the pdInfoBuilder
vignette.
b
On Mon, Mar 1, 2010 at 8:55 PM, somnath bandyopadhyay <
genome1976@hotmail.com> wrote:
> Thanks for the info. What is the COUNT column?
>
> These are the columns in my *.pair files:
>
>
> IMAGE_ID GENE_EXPR_OPTION SEQ_ID PROBE_ID POSITION X Y MATCH_INDEX
SEQ_URL PM MM
>
> Thanks,
> Som.
> MATCH_INDEX SEQ_URL PM MM
> > From: beniltoncarvalho@gmail.com
> > Date: Mon, 1 Mar 2010 20:39:47 +0000
> > Subject: Re: [BioC] makePDpackage
>
> > To: genome1976@hotmail.com
> > CC: bioconductor@stat.math.ethz.ch
> >
> > Hi Som,
> >
> > use the pdInfoBuilder package instead.
> >
> > About PAIR -> XYS... you need to create a text file with the
following
> > columns (X/Y/SIGNAL/COUNT). It should be sorted by X and Y
coordinates
> > and control probes should have NA in the SIGNAL column. All X/Y
> > coordinates should be included.
> >
> > X Y SIGNAL COUNT
> > 1 1 321.12 1
> > 1 2 NA 1
> > 1 3 123.34 1
> > .. .. .....
> >
> > The XYS files can be generated directly from NimbleScan....
> >
> > b
> >
> > On Mon, Mar 1, 2010 at 8:27 PM, somnath bandyopadhyay
> > <genome1976@hotmail.com> wrote:
> > >
> > > Hi,
> > >
> > > I am trying to annotate the Nimblegen 385k mm8 refseq promoter
chip
> and the following is what I have been using:
> > >
> > >
> > >
> > >> makePDpackage("2006-07-18_MM8_RefSeq_promoter.ndf", "FILE.XYS",
> "2006-07-18_MM8_RefSeq_promoter.pos",manufacturer="nimblegen",
> type="expression", genomebuild = "mm8")
> > > nimblegen expression
> > > The package will be called pd.2006.07.18.mm8.refseq.promoter
> > > Reading 2006-07-18_MM8_RefSeq_promoter.ndf
> > > Assuming a simple design (NOT multiple-wells).
> > > Correcting probe positions... Done.
> > > Error in getClass(Class, where = topenv(parent.frame())) :
> > > "platformDesign" is not a defined class
> > >
> > >
> > >
> > > Could anybody help me out with this? Moreover, is there a way to
> convert .pair files into .XYS files for nimblegen?
> > >
> > >
> > >
> > > Thank so much,
> > >
> > > Som.
> > >
> > >
_________________________________________________________________
> > > Hotmail: Trusted email with powerful SPAM protection.
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
>
> ------------------------------
> Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. Sign
up
> now. <http: clk.atdmt.com="" gbl="" go="" 201469229="" direct="" 01=""/>
>
[[alternative HTML version deleted]]
