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Christopher N Barnes | 4 Dec 21:30
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Cannot read in CEL files with XPS

All,

I am new to xps and am having trouble reading in the cel files.

I got the 3 correct files from affymetrix and created a scheme removing the first 12 lines from the
annotation  file (fix 1)

 
I then read in my scheme:
hgu133plus2<-root.scheme(paste(.path.package("xps"),"schemes/hgu133plus2.root",
   sep="/"))

and then try to read in the CEL files.
celdir2<-"C:/McMasters/test"
data.test3<-import.data(hgu133plus2,"tmp2",celdir=celdir2, verbose=FALSE)
It worked 1 time and now causes R to crash.  I am trying to read in 40 CEL files 50,000+ genes on a 4G machine.

Does anyone have any suggestions of another method to read a large amount of CEL files.  If I try using Read
Affy()  to read in, I don't have the space to allocate.  

Thanks for the  Help,

Chris Barnes
PhD student 
University of Louisville

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Emanuele Marchi | 4 Dec 16:15
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subsetting lumibatch object by probe ID

Hi Everybody,
I have a list of illumina probe ID's (ILMN_#####) and I'd like to subset 
the matrix of expression values (exprs(lumi.batch.object) by probe ID, 
i.e. row names.
Is there an obvious (and quick) sub-setting method to do that?

If I use plotSampleRelation I can choose a selection of probes (selProbe 
parameter) but I guess it has to be as numeric vector, am I correct?
In fact I tried to put the character vector containing probeID/row names 
and it didn't work...
thank you and really sorry if the question is too basic for you...

Regards,

Emanuele

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T Joshi | 4 Dec 14:37

biomaRt with multiple databases/datasets?

Hi,
I was wondering if it is possible to use biomaRt package with multiple
databases and hence datasets. I want to retrieve GO information using
ensembl geneIDs. I use the following :

attributes=c("ensembl_gene_id","go_biological_process_id","go_cellular_component_id",
"go_biological_process_id", "go_biological_process_linkage_type",
"go_cellular_component_linkage_type","go_molecular_function_linkage_type"),

 and filters="ensembl_gene_id", for a "mart" object which uses ensembl
database.

I would like to see the names of pathways and reactions in which this
gene is involved. Could we do so using biomaRt?

cheers,
Josh

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T Joshi | 4 Dec 14:23

Re: error with getBM function of biomaRt package

Hi,
Thank you James, Installing RCurl package again solved the problem.

Josh

On Wed, Dec 3, 2008 at 2:25 PM, James W. MacDonald
<jmacdon@...> wrote:
> Hi Josh,
>
> The version of RCurl that you have seems to be really old to me. The version
> used by BioC 2.3 is 0.92-0. You might try biocLite("RCurl"), or better yet,
> upgrade to R-2.8.0 and BioC 2.3.
>
> Best,
>
> Jim
>
>
>
> T Joshi wrote:
>>
>> Hi,
>> I was running the example in getBM and got the following error:
>>
>>
>> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"),
>> mart=mart)
>> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
>> "chromosome_name",  :
>>  could not find function "postForm"
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Sean Davis | 3 Dec 12:20

Re: biomaRt getSequence through genomic position

On Tue, Dec 2, 2008 at 11:18 PM,  <steffen@...> wrote:
> Hi Paul,
>
> To retrieve sequences with biomaRt and mysql=TRUE, the package actually
> connects to two BioMarts one is Ensembl and the other is the sequence
> BioMart.  However the user only needs to connect to the Ensembl BioMart.
> Under the hood getSequence will also connect to the sequence BioMart.  It
> looks like it doesn't disconnect and this causes the error when you apply
> this in a loop.  I'll try to provide a fix as soon as possible.
>
> Unfortunately it is not possible to retrieve genomic sequences with mysql=F.
> We need to discuss with the Ensembl developers and ask them if they could
> make this available through their BioMart web service.
>
> Cheers,
> Steffen
>
>> Dear Paul,
>>
>> and what is the output of sessionInfo()?
>>
>>   bw Wolfgang
>>
>> Paul Hammer ha scritto:
>>> hi all,
>>>
>>> i try to get sequences via the getSequence function from biomaRt. Exact
>>> i would like to have the last 5 bases of an exon and the last 5 bases of
>>> the following intron. my approach is following:
>>>
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James W. MacDonald | 2 Dec 22:30

Re: makecdfenv crashes

Hi Aaron,

Skewes,Aaron wrote:
> Hi,
> 
> I am attempting to make a CDF package for Affy GenomeWideSNP 6.0 platform using makecdfenv, and it
crashes. Any suggestions?

Yes. Don't do that ;-D

You want to use oligo for the analysis of the SNP6.0 data. This package 
doesn't use a cdf package - instead it uses a pdInfoPackage, which you 
can get via biocLite("pd.genomewidesnp.6").

Best,

Jim

> 
> Thanks,
> Aaron
> 
>> library("makecdfenv")
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
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Naomi Altman | 2 Dec 15:42

Re: cDNA raw intensities

Dear Santana

This does not really help much, because the "normalized expression" 
depends on the treatment.  Do both channels have the same 
treatment?  Is this a reference design?

Anyways, to do what you want, what I generally do is use cbind to 
merge the expression values with the annotation information and 
write.csv to write a comma separated table which can be read into a 
spreadsheet such as Excel.  I do not expect to be able to do all my 
processing in R.  However, some of the R gurus on the list can 
probably do everything in R.  I meant
to cc the list when I first wrote, and I am returning this to you.

Best of luck,
Naomi

At 04:31 AM 12/2/2008, you wrote:

>Hi Naomi,
>
>Thanks for your prompt reply !
>
>Well, I wanted to experiment something, and accordingly thought that 
>I would examine the individual raw data. But I believe, I should 
>follow the conventional way, atleast for the time-being.
>
>Anyways, even then I have a bit of problem.
>
>I am uncertain as to how I can have each gene's normalised
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James W. MacDonald | 2 Dec 15:32

Re: Mouse Gene ST v1 CDF Issues (MoGene10stv1): Failure of affyPLM and pdfInfoBuilder

Hi Peter,

I won't comment on aroma.affymetrix, nor building cdf packages using 
makecdfenv as the former has its own mailing list and the latter isn't 
really supported - the list archive you quote is Ben Bolstad showing 
that you _could_ use makecdfenv, but then raising several questions that 
have not been resolved to my knowledge.

As for building a pdInfoPackage, this works fine for me:

 > makePdInfoPackage(pkg, destDir=".")
Creating package in ./pd.mogene.1.0.st.v1
loadUnitsByBatch took 46.92 sec
loadAffyCsv took 19.19 sec
loadAffySeqCsv took 51.92 sec
DB sort, index creation took 20.82 sec
[1] TRUE
Warning messages:
1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
 > sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
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Renaud Gaujoux | 2 Dec 09:21

Re: Illumina annotation packages discrepancy

I just had a quick try but just got NAs. Should the code below work with 
this package?

entrez <- getEG(probeids, 'illuminaHumanv2ProbeID.db')

which wraps:

unlist(lookUp(probeids, 'illuminaHumanv2ProbeID.db', "ENTREZID"))

I tried with probeids being Illumina full IDs, Illumina trimmed IDs 
(without ILMN_), and with nuIDs.

Thanks,
Renaud

Lynn Amon wrote:
> You'll want to use the illuminaHumanv2ProbeID.db package.
> Lynn
>
> Renaud Gaujoux wrote:
>> Oups... I'm really sorry Mark for the confusion. I think misread the 
>> vignette.
>>
>> I BLASTed some of the missing probes and some of them gave quite 
>> convincing results (100% identity but with different variants), 
>> others didn't return any sequence. So I'll try with the package from 
>> 2.2.
>>
>> Thanks again,
>> Renaud
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Patrick Aboyoun | 1 Dec 21:58
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Votes for biocLite "default" group modifications

BioC Community,
As part of a routine project maintenance effort, we are evaluating the 
packages within "default" group in biocLite to ensure we are adequately 
representing a base installation of Bioconductor. There are currently 29 
packages, plus their dependencies, that are installed when biocLite() is 
called with no arguments:

 > source("http://bioconductor.org/biocLite.R")
 > biocinstallPkgGroups()
 [1] "affy"         "affydata"     "affyPLM"      "annaffy"    
 [5] "annotate"     "Biobase"      "Biostrings"   "DynDoc"     
 [9] "gcrma"        "genefilter"   "geneplotter"  "hgu95av2.db"
[13] "limma"        "marray"       "matchprobes"  "multtest"   
[17] "ROC"          "vsn"          "xtable"       "affyQCReport"
[21] "edd"          "globaltest"   "makecdfenv"   "pamr"       
[25] "siggenes"     "sma"          "statmod"      "tkWidgets"  
[29] "widgetTools"

How well do you think this list refects the core of Bioconductor 
functionality? In order to avoid unnecessary conflict amongst the user 
community, please send me a private e-mail stating which packages you 
believe should be included in and/or removed from the "default" list. In 
a few weeks I will send a follow up email that summarizes our findings. 
In order to guide your responses, you can refer to the package download 
stats located at

http://bioconductor.org/packages/stats

Thanks in advance for any assistance you can provide.
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