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

Thanks a lot,
Suparna

On 4 September 2012 18:10, James W. MacDonald <jmacdon@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@uw.edu <mailto:
>> jmacdon@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@uw.edu
>>         <mailto:jmacdon@uw.edu> <mailto:jmacdon@uw.edu
>>
>>         <mailto:jmacdon@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]]
>>
>>                 ______________________________**_________________
>>                 Bioconductor mailing list
>>         Bioconductor@r-project.org <mailto:Bioconductor@r-**project.org<Bioconductor@r-project.org>
>> >
>>         <mailto:Bioconductor@r-**project.org <Bioconductor@r-project.org>
>>
>>         <mailto:Bioconductor@r-**project.org <Bioconductor@r-project.org>
>> >>
>>
>>         https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>                 Search the archives:
>>         http://news.gmane.org/gmane.**science.biology.informatics.**
>> conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>>
>>             --     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@liverpool.ac.uk
>>         <mailto:smitra@liverpool.ac.uk**> <mailto:smitra@liverpool.ac.uk
>>
>>         <mailto:smitra@liverpool.ac.uk**>>
>>         Alternative Email id: suparna.mitra.sm@gmail.com
>>         <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com>
>> >
>>         <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@gmail.com>
>>
>>         <mailto:suparna.mitra.sm@**gmail.com <suparna.mitra.sm@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@liverpool.ac.uk <mailto:smitra@liverpool.ac.uk**>
>> Alternative Email id: suparna.mitra.sm@gmail.com <mailto:
>> suparna.mitra.sm@**gmail.com <suparna.mitra.sm@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@liverpool.ac.uk
Alternative Email id: suparna.mitra.sm@gmail.com

	[[alternative HTML version deleted]]

