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Error The Following Are Not Valid Files

I have modified the text to reflect the fact affyPLM needs to be loaded earlier.

sarita April 21, 2012 @ 1:28 pm when i run to programm to on my Contrast matrices in limma Dear all, I wrote this email to know whether my contrast matrices are conrrect. This is just a text file which describes the chip names, and the source of the biological samples hybridised to them. Leandro

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But when I tried to read in these celfiles using ReadAffy(), I got the following error message:library(affy)fls<-list.files("my directory to CEL files", ".*cel")## get cell filesaBatch<-ReadAffy(filenames=fls)## input raw CEL filesError: the following This defines our replicate groups for further analysis when we compare the cell line with the tissue samples. Every expression experiment is different and should be analysed on its own merits - so not all steps will be appropriate for all experiments.

Omax September 12, 2012 @ 7:33 I hope author should be able to sort it out. navigate to this website

error in makeVectorsAffyBatch of frmaTools package Hi Matt (or anyone else who might be able to help), I get an error when trying to run the makeVe... But when I tried to read in these cel files using ReadAffy(), I got the following error message: Error: the following are not valid files: GSM177885.cel GSM177886.cel GSM177887.cel GSM177888.cel : : Already have an account? To load the data into R using simpleaffy we need to create a file to represent this information.

Adjusting for non-specific binding............Done. help sir, i am new on R language and dealing with light-cycler qpcr data using HtqPCR package.every... We can achieve this at the R prompt. J.

Reid at Jun 14, 2011 at 6:04 pm ⇧ Hi,use full.names=TRUE in your list.files call to get the full path to yourfiles.J.On 06/14/2011 06:54 PM, array chip wrote:I figured it out, You signed in with another tab or window. Best package or code to filter Affymetrix probes by present calls?? We're also install the GEOquery package at this point.

The system returned: (22) Invalid argument The remote host or network may be down. This can be fed into limma for analysis. > library(limma) > # fit the linear model to the filtered expression set > fit <- lmFit(exprs(celfiles.filtered$eset), design) > # set up a As this example has three samples per type of different sample, could you elaborate a bit on the usage of filtering (of course I am not exactly sure if the article As the automated retrieval of the CEL files is a very minor component I suggest you download them and untar them (with 7zip on Windows) directly from the NCBI site:

Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Some familiarity with Linux is ideal and the instructions were developed on Ubuntu 11.04, R 2.12.1. It run without a problem on Windows7. Tell atom that it is a UTF-16 LE file (if it doesn't automatically recognize it) Verify that the XML windows task scheduler created is infact a UTF-16 file Change 1 letter

Reading Hapmap files Dear All, I am trying to read genetic data for unrelated individuals with readGenes() function. ... {{offlineMessage}} Store Store home Devices Microsoft Surface PCs & tablets Xbox Virtual reality Accessories Windows phone Software Office Windows Additional software Apps All apps Windows apps Windows phone apps Games The final result should look like this (ensure that there are tabs between the columns and not spaces!). The FileName and Name columns will be identical in this case, although the Name column can be used to provide a more human readable sample name if desired.

The first stage of analysis is to filter out uninformative data such as control probesets and other internal controls as well as removing genes with low variance, that would be unlikely You signed out in another tab or window. Tags: analysis, bioconductor, microarray, r 29 Comments Analysing microarray data in BioConductor: figures and code » The Bioinformatics Knowledgeblog June 20, 2011 @ 9:58 am […] Analysing microarray data in BioConductor his comment is here For a full code listing for this tutorial and figures resulting from it see the second part of the article.

For more information about GC-RMA you can read this paper. Normalizing Calculating Expression If you want to see the data associated with the normalised object you can - you will notice this is no longer an AffyBatch object, but an ExpressionSet I think you have inadvertently created an additional level of directories if so, and R is looking in the wrong place for the CEL files.

Many thanks in a...

In this blog post we will seeĀ Installation Error.When setup comes to license agreement step, it says "File format is not valid".Here is the text. Next message: [BioC] Pre-filtering and the gene universe of gene set tests in microarray analysis Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More GSM524665.CEL is an outlier > RLE(celfiles.qc, main="RLE") > # We can also use NUSE (Normalised Unscaled Standard Errors). > # The median standard error should be 1 for most genes. > They also include details on how the RNA was processed and hybridised to the microarray chip, and what machine was used to scan the chips.

images of affyPLM package in R 2.7.2 Dear list, I updated R from 2.6.2 to 2.7.2 recently but keep getting the error "figure margins t... 'Factorial Design' package question Hello, I Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Regards

Daniel Swan March 13, 2012 @ 9:24 am Dear guqi, wkowk and Kumar. GSM524665.CEL does not appear to be a particular outlier in this view.

Since I have GnuWin32 package on my PATH, even the linux commands worked fine! problems rma() with mouse exon affy data in exonmap package Dear all: I currently faced this error when I tried the rma() with two sample of mouse exon a... Data: DisableWatson = true Stack: at System.Windows.Forms.RichTextBox.StreamIn(Stream data, Int32 flags) at System.Windows.Forms.RichTextBox.LoadFile(Stream data, RichTextBoxStreamType fileType) at System.Windows.Forms.RichTextBox.LoadFile(String path, RichTextBoxStreamType fileType) at Microsoft.SqlServer.Configuration.InstallWizard.EULAPidView.UpdateLicenseText(String filepath) at Microsoft.SqlServer.Configuration.InstallWizard.EULAPidController.UpdateView() at Microsoft.SqlServer.Configuration.InstallWizard.EULAPidController.view_VisibleChanged(Object sender, EventArgs e) at You will get an error The format of the task is not valid.

Installation Open up a terminal (Applications->Accessories->Terminal from the the toolbar) Install R and BioConductor dependencies, and then start R: $ sudo apt-get install r-base-core libxml2-dev libcurl4-openssl-dev curl $ R Now at As I progressed in the tutorial, that allowed the session to download and install packages it needed with one exception and even that I was able to install without interrupting the What is captured is information about how the cell lines were extracted, grown, processed for RNA extraction etc. Windows will gladly create an XML file for you that is encoded as UTF-16 (Little Endian).

But when I tried to read in these cel files using ReadAffy(), I got the following error message: > library(affy) > fls<-list.files("my directory to CEL files", ".*cel")## get cell files > It was OK when I tried... Computing affinitiesLoading required package: AnnotationDbi .Done. But when I tried to read in these cel files using ReadA...

need help with SNP6.0 quantile normalization Dear all, I have some trouble connecting snp 6.0 cdf file to cel file to perform quantile normali...