[BioC] Beadarray expression data

[Yogi Sundaravadanam]

Sorry Simon, that was meant for Ina

Cheers
 
 
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Yoganand Sundaravadanam
Bioinformatics Officer
Australian Genome Research Facility Ltd
Level 5 Gehrmann Laboratories
Research Road
University of Queensland
St Lucia QLD
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Fax: +61 7 3365 1823
Email: yogi.sundaravadanam at agrf.org.au
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-----Original Message-----
From: Yogi Sundaravadanam 
Sent: Wednesday, 8 August 2007 9:07 AM
To: bioconductor; simonlaw23
Subject: Re: [BioC] Beadarray expression data


Hello Simon

If you are using beadarray package, you first have to read the data file into an object, like this

data<-read.csv("data_file.csv", skip=7) 
You have got to skip the first 7 rows as these just contain general information.

To select a set of columns which is required for the analysis step, you can use the function subset.

Expression <- subset(data, select = grep("AVG", names(data))) The above line selets all the columns starting with their names as AVG

Beads <- subset(data, select = grep("Avg", names(data)))
This selects all columns that start with Avg


Hope this helps?
Yogi

 
 
  _____  

Yoganand Sundaravadanam
Bioinformatics Officer
Australian Genome Research Facility Ltd
Level 5 Gehrmann Laboratories
Research Road
University of Queensland
St Lucia QLD
Phone: +61 7 3346 7328
Fax: +61 7 3365 1823
Email: yogi.sundaravadanam at agrf.org.au
Web: www.agrf.org.au
Subscribe to the AGRF Newsletter  
  _____  

 Please Note: The message is intended only for the addressee. If you receive this message in error please do not publish, distribute, or copy it. Please advise the AGRF by telephone or email, and delete this message from your computer. 

-----Original Message-----
From: simonlaw23 at hotmail.com [mailto:simonlaw23 at hotmail.com] 
Sent: Wednesday, 8 August 2007 7:28 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Beadarray expression data

Ina Hoeschele <inah at ...> writes:

> 
> Hi all,
>    I am completely new to the analysis of Illumina Beadarray gene 
> expression data (but quite familiar with Affy data).  Such data (with 
> samples run on 3 chips)  was sent to me by a collaborator. From the 
> vignettes for Bioconductor packages 'beadarray' and 'BeadExplorer', it 
> looks like these accommodate  Beadstudio version 1 and 2 data, while our 
> data was created by BeadStudio version  3.0.14.. Would it still work? My 
> collaborator sent two types of files to me: (1) a number of .csv files 
> (read by excel, 2 for each sample) with columns Illumicode, N, mean GRN, 
> Dev GRN. (2) a summary .txt file with columns TargetID    
> MIN_Signal-1814647013_A    AVG_Signal-1814647013_A    
> MAX_Signal-1814647013_A    NARRAYS-1814647013_A    
> ARRAY_STDEV-1814647013_A    BEAD_STDEV-1814647013_A    
> Avg_NBEADS-1814647013_A    Detection-1814647013_A, with the 
> MIN_Signal-... to Detection-... columns repeated for the remaining samples.
> It looks like beadarray expects to read the summary data from a .csv 
> rather than a .txt file? From the example given on page 2 of the 
> beadarray vignette, the summary data are read in by
> BSData <- readBeadSummaryData(datafile, ..., columns = list(exprs = 
> AVG_Signal", BeadStDev = "BEAD_STDEV", NoBeads = "Avg_NBEADS", ...)
> 
> Since I have AVG_Signal-1814647013_A, AVG_Signal-1814647013_B etc. and 
> not just one AVG_Signal, how do I specify the columns to be read?
> 
> Sorry for these ignorant questions, but this is my first try at these 
> data. Thanks for any advice!
> Ina
> 
> _______________________________________________
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http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 

Hi Ina, 

I used beadarray version 1.2.2 and my bead summary data were from BeadStudio V2.
I don't think the BeadStudio version should not be a concern when extracting the
bead summary data from the raw data file (either .txt or csv file). Your data
are summary data because of the column "AVG_Signal-", readBeadSummaryData()
function reads in all the columns begin with "AVG_Signal-" from the summary data
file and create a BSData object for further preprocessing steps. If you still
concern about the version compatibility, you can use something like
read.table/read.csv to extract the raw summary data (all columns start with
"AVG_Signal-") and compare the result to the BSData object that you obtained
from using readBeadSummaryData() function.

Regarding how to use the readBeadSummaryData() function in beadarray, if you set
everything correct in the target file, in which you need to name the path of
your raw data file and other information for the data set (refer to beadarray
vignette for details), you don't need to pass anything for the parameter
columns. The function knows what to do with the columns in the data file.

Best,

Simon

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