[BioC] Error in setQCEnvironment(cdfn)
James W. MacDonald
jmacdon at uw.edu
Tue Sep 4 19:19:56 CEST 2012
Hi Suparna,
On 9/4/2012 1:14 PM, suparna mitra wrote:
> Hi Jim,
> Thanks a lot, but the files are there and also I just figured out
> somehow is working with "=".
> InVivodat=read.celfiles(list.celfiles("/Users/smitra/Desktop/Recent/Micro_RawData/InVivoTargets/"))
> No idea why. But now I get:
> Loading required package: pd.hugene.1.0.st.v1
> Attempting to obtain 'pd.hugene.1.0.st.v1' from BioConductor website.
> Checking to see if your internet connection works...
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.12
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.12
> trying URL
> 'http://bioconductor.org/packages/2.7/data/annotation/bin/macosx/leopard/contrib/2.12/pd.hugene.1.0.st.v1_3.0.2.tgz'
> Content type 'application/x-gzip' length 68064870 bytes (64.9 Mb)
> opened URL
> =================================================
> downloaded 64.9 Mb
>
>
> The downloaded packages are in
> /var/folders/yq/fb09p6c556lf48k41ntj6v4w0000gp/T//RtmpPDzMft/downloaded_packages
> Loading required package: pd.hugene.1.0.st.v1
> Platform design info loaded.
> Reading in : MC1_(HuGene-1_0-st-v1).CEL
> Reading in : MC10_(HuGene-1_0-st-v1).CEL
> Reading in : MC11_(HuGene-1_0-st-v1).CEL
> Reading in : MC12_(HuGene-1_0-st-v1).CEL
> Reading in : MC13_(HuGene-1_0-st-v1).CEL
> Reading in : MC14_(HuGene-1_0-st-v1).CEL
> Reading in : MC15_(HuGene-1_0-st-v1).CEL
> Reading in : MC16_(HuGene-1_0-st-v1).CEL
> Reading in : MC17_(HuGene-1_0-st-v1).CEL
> Reading in : MC18_(HuGene-1_0-st-v1).CEL
> Reading in : MC2_(HuGene-1_0-st-v1).CEL
> Reading in : MC3_(HuGene-1_0-st-v1).CEL
> Reading in : MC4_(HuGene-1_0-st-v1).CEL
> Reading in : MC5_(HuGene-1_0-st-v1).CEL
> Reading in : MC6_(HuGene-1_0-st-v1).CEL
> Reading in : MC7_(HuGene-1_0-st-v1).CEL
> Reading in : MC8_(HuGene-1_0-st-v1).CEL
> Reading in : MC9_(HuGene-1_0-st-v1).CEL
> Warning message:
> In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, :
> there is no package called 'pd.hugene.1.0.st.v1'
>
> So now I am trying to find pd.hugene.1.0.st.v1
It's there. That warning gets propagated incorrectly. You can see by doing
search()
at your R prompt.
Best,
Jim
>
> Thanks a lot,
> Suparna
>
> On 4 September 2012 18:10, James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>> wrote:
>
> Hi Suparna,
>
> If the files aren't in your working directory, you need to add
> that information to your call to read.celfiles.
>
> read.celfiles(filenames =
> paste("/Users/smitra/Desktop/Micro_RawData/InVivoTargets/",
>
> list.celfiles("/Users/smitra/Desktop/Micro_RawData/InVivoTargets"), sep
> = "")
>
>
> Best,
>
> Jim
>
>
>
> On 9/4/2012 12:59 PM, suparna mitra wrote:
>
> Hello Jim,
> Thanks a lot for your reply and help. But now it seems I am
> having a new problem with read.celfiles.
> Until now ReadAffy worked perfectly, but not read.celfiles. It
> tells the proper files names but says "Error: These do not
> exist:" as shown below. Am I doing any silly mistake?
>
> Any help will be really great.
> Thanks a lot,
> Suparna.
>
> > mydata <- ReadAffy()
>
> > mydata
>
> AffyBatch object
>
> size of arrays=1050x1050 features (13 kb)
>
> cdf=HuGene-1_0-st-v1 (32321 affyids)
>
> number of samples=12
>
> number of genes=32321
>
> annotation=hugene10stv1
>
> notes=
>
>
> >
> InVivodat<-read.celfiles(list.celfiles("/Users/smitra/Desktop/Micro_RawData/InVivoTargets"))
>
> Error: These do not exist:
>
> MC1_(HuGene-1_0-st-v1).CEL
>
> MC10_(HuGene-1_0-st-v1).CEL
>
> MC11_(HuGene-1_0-st-v1).CEL
>
> MC12_(HuGene-1_0-st-v1).CEL
>
> MC13_(HuGene-1_0-st-v1).CEL
>
> MC14_(HuGene-1_0-st-v1).CEL
>
> MC15_(HuGene-1_0-st-v1).CEL
>
> MC16_(HuGene-1_0-st-v1).CEL
>
> MC17_(HuGene-1_0-st-v1).CEL
>
> MC18_(HuGene-1_0-st-v1).CEL
>
> MC2_(HuGene-1_0-st-v1).CEL
>
> MC3_(HuGene-1_0-st-v1).CEL
>
> MC4_(HuGene-1_0-st-v1).CEL
>
> MC5_(HuGene-1_0-st-v1).CEL
>
> MC6_(HuGene-1_0-st-v1).CEL
>
> MC7_(HuGene-1_0-st-v1).CEL
>
> MC8_(HuGene-1_0-st-v1).CEL
>
> MC9_(HuGene-1_0-st-v1).CEL
>
> >
>
>
> On 4 September 2012 17:27, James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu> <mailto:jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>>> wrote:
>
> Hi Suparna,
>
> I use the oligo package to analyze these data, rather than the
> affy package. I also use my affycoretools package to help make
> certain QC plots that I like.
>
> I tend to do something like
>
> dat <- read.celfiles(list.celfiles(<wherever they are>))
> hist(dat) ## gives a density plot - they should all look
> similar
>
> You can look for problematic arrays using a probe level
> model. If
> you have multiple cores, you can first do
> Sys.setenv(R_THREADS = <number of cores you want to use>)
> plm <- fitProbeLevelModel(dat)
>
> Then you can look at
> NUSE(plm)
> RLE(plm)
>
> It may also be interesting to look at residuals
> image(plm, type="residuals")
>
> Then
> eset <- rma(dat)
>
> If you use affycoretools you can do
>
> plotPCA(eset, <vector of numbers indicating group membership>,
> <group types>)
>
> and see if your replicates are grouping together. You can
> also do
> MA plots
>
> maplot(eset)
>
> which compare all your chips to a pseudo-array. If you
> have more
> than 25 arrays, you should do 25 at a time.
>
> Note that if you use the limma package to make comparisons
> you can
> weight arrays, so unless one or more are completely
> broken, you
> usually don't need to exclude. It's instructive to add the
> weights
> to a PCA plot. So if you have say 3 treated vs 3 control, you
> could do something like
>
> trt <- factor(rep(c("Treated","Control"), each = 3))
> design <- model.matrix(~trt)
> wts <- arrayWeights(eset, design)
>
> plotPCA(eset, groups, groupnames, addtext = round(wts, 2))
>
> Best,
>
> Jim
>
>
> On 9/4/2012 12:06 PM, suparna mitra wrote:
>
> Dear Jim,
> Thanks a lot. Yes I also read something that HuGene
> array
> does not use the T7-Oligo(dT) primer. But sorry being
> new I
> just missed the point. Actually I was trying to follow
> a step
> by step tutorial for Affy data.
>
> But can you suggest the best way to perform qc for
> this chip?
> Thanks a lot,
> Suparna.
>
> On 4 September 2012 16:58, James W. MacDonald
> <jmacdon at uw.edu <mailto:jmacdon at uw.edu>
> <mailto:jmacdon at uw.edu <mailto:jmacdon at uw.edu>>
> <mailto:jmacdon at uw.edu <mailto:jmacdon at uw.edu>
>
> <mailto:jmacdon at uw.edu <mailto:jmacdon at uw.edu>>>> wrote:
>
> Hi Suparna,
>
>
> On 9/4/2012 11:35 AM, suparna mitra wrote:
>
> Hello group,
> I am new in bioconductor and trying use it
> for my
> Affymetrix
> microarray
> data.
> Genechip HuGene-1_0-st-v1.
>
>
> The simpleaffy package isn't really designed for
> this array. A
> significant portion of the QC measures are based on
> comparisons
> between the PM and MM probes, and the newer
> generation of
> arrays
> from Affy no longer have MM probes.
>
> Best,
>
> Jim
>
>
>
> I have normalized my data using rma. Then when I
> trying to see
> the quality
> I found following error. Can anybody help me
> with this
> please.
> Thanks a lot in advance :)
> Best wishes,
> Suparna.
>
> library(affy)
> library(simpleaffy)
>
> Loading required package: genefilter
> Loading required package: gcrma
>
> Attaching package: 'simpleaffy'
>
> The following object(s) are masked _by_
> '.GlobalEnv':
>
> getBioC
>
> library("hugene10stv1cdf")
> aqc<-qc(InVivodata)
>
> Error in setQCEnvironment(cdfn) :
> Could not find array definition file '
> hugene10stv1cdf.qcdef '.
> Simpleaffy does not know the QC parameters for
> this
> array type.
> See the package vignette for details about how to
> specify QC
> parameters
> manually.
>
> [[alternative HTML version deleted]]
>
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>
> -- James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
>
> -- Dr. Suparna Mitra
> Wolfson Centre for Personalised Medicine
> Department of Molecular and Clinical Pharmacology
> Institute of Translational Medicine University of
> Liverpool
> Block A: Waterhouse Buildings, L69 3GL Liverpool
>
> Tel. +44 (0)151 795 5394
> <tel:%2B44%20%280%29151%20795%205394>
> <tel:%2B44%20%280%29151%20795%205394>, Internal ext: 55394
> M: +44 (0) 7511387895
> <tel:%2B44%20%280%29%207511387895>
> <tel:%2B44%20%280%29%207511387895>
> Email id: smitra at liverpool.ac.uk
> <mailto:smitra at liverpool.ac.uk>
> <mailto:smitra at liverpool.ac.uk
> <mailto:smitra at liverpool.ac.uk>>
> <mailto:smitra at liverpool.ac.uk <mailto:smitra at liverpool.ac.uk>
>
> <mailto:smitra at liverpool.ac.uk <mailto:smitra at liverpool.ac.uk>>>
> Alternative Email id: suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>
> <mailto:suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>>
> <mailto:suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>
>
> <mailto:suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>>>
>
>
> -- James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
>
> --
> Dr. Suparna Mitra
> Wolfson Centre for Personalised Medicine
> Department of Molecular and Clinical Pharmacology
> Institute of Translational Medicine University of Liverpool
> Block A: Waterhouse Buildings, L69 3GL Liverpool
>
> Tel. +44 (0)151 795 5394
> <tel:%2B44%20%280%29151%20795%205394>, Internal ext: 55394
> M: +44 (0) 7511387895 <tel:%2B44%20%280%29%207511387895>
> Email id: smitra at liverpool.ac.uk
> <mailto:smitra at liverpool.ac.uk> <mailto:smitra at liverpool.ac.uk
> <mailto:smitra at liverpool.ac.uk>>
> Alternative Email id: suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>
> <mailto:suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
>
> --
> Dr. Suparna Mitra
> Wolfson Centre for Personalised Medicine
> Department of Molecular and Clinical Pharmacology
> Institute of Translational Medicine University of Liverpool
> Block A: Waterhouse Buildings, L69 3GL Liverpool
>
> Tel. +44 (0)151 795 5394, Internal ext: 55394
> M: +44 (0) 7511387895
> Email id: smitra at liverpool.ac.uk <mailto:smitra at liverpool.ac.uk>
> Alternative Email id: suparna.mitra.sm at gmail.com
> <mailto:suparna.mitra.sm at gmail.com>
>
--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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