Go Back   Science Forums Biology Forum Molecular Biology Forum Physics Chemistry Forum > Molecular Research Topics Forum > Omics and Genomics Forum > Microarrays Forum
Register Search Today's Posts Mark Forums Read

Microarrays Forum Microarray Forum. Discuss array technology and Gene Chips. DNA microarray and Protein arrayit forums.


DNA Microarray analysis help please!

DNA Microarray analysis help please! - Microarrays Forum

DNA Microarray analysis help please! - Microarray Forum. Discuss array technology and Gene Chips. DNA microarray and Protein arrayit forums.


Reply
 
LinkBack Thread Tools Display Modes
  #1  
Old 01-03-2006, 09:41 AM
Pipette Filler
Points: 2,448, Level: 31 Points: 2,448, Level: 31 Points: 2,448, Level: 31
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Jan 2006
Posts: 27
Thanks: 0
Thanked 5 Times in 5 Posts
Talking DNA Microarray analysis help please!



I need DNA Microarray analysis help please!

I have generated data but I need software for statistical analysis.
Please help,
thanks in advance!
Reply With Quote
  #2  
Old 01-08-2006, 10:50 AM
Pipette Filler
Points: 2,662, Level: 33 Points: 2,662, Level: 33 Points: 2,662, Level: 33
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Jan 2006
Posts: 27
Thanks: 0
Thanked 0 Times in 0 Posts
Lightbulb Several Bioinformatic Programs

Several Bioinformatic Programs for your analysis:
[Only registered users see links. ]

[Only registered users see links. ]


Cheers
Reply With Quote
  #3  
Old 02-02-2006, 06:13 AM
admin's Avatar
Administrator
 
Join Date: Nov 2005
Posts: 1,418
Thanks: 883
Thanked 68 Times in 58 Posts
Default see Microarray Station

Hey Guys, look for upcoming articles at our new website:
Microarray Station

Also, there are sections there that have many bioinformatic programs and software. I am not exactly an expert at analyzing microarray data although I have some ideas...however the people working on those sites are. There should be a forum up there or it will link here and you can get help from them.

Cheers.
Reply With Quote
  #4  
Old 08-04-2006, 05:52 PM
Aristotle's Avatar
Pipette Filler
Points: 1,992, Level: 27 Points: 1,992, Level: 27 Points: 1,992, Level: 27
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Aug 2006
Posts: 15
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: DNA Microarray analysis help please!

Are there any tutorials to help in the analysis of microarrays?

thanks
Reply With Quote
  #5  
Old 10-04-2006, 08:21 PM
Pipette Filler
Points: 1,709, Level: 25 Points: 1,709, Level: 25 Points: 1,709, Level: 25
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Oct 2006
Location: Germany
Posts: 1
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: DNA Microarray analysis help please!

Hello
I read article about microarray. Could you tell me what 22K or 44K array means? and what "spike-in" means?

please
Reply With Quote
  #6  
Old 10-04-2006, 11:47 PM
oBWhat's Avatar
Graduate Student
Points: 3,826, Level: 41 Points: 3,826, Level: 41 Points: 3,826, Level: 41
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: May 2006
Posts: 124
Thanks: 0
Thanked 7 Times in 7 Posts
Default Re: DNA Microarray analysis help please!

Hey Signal,
22k and 44k probably refer to the number of capture molecules (primers or cDNA capture molecules) located on the array. They can be even overlapping primers / cDNAs, or even primers that act as controls for other primers (ie to test background).

There can be 1-100 primers for a single gene (cDNA), so the 44K is quite large.
Reply With Quote
  #7  
Old 11-27-2006, 04:58 AM
Pipette Filler
Points: 1,654, Level: 24 Points: 1,654, Level: 24 Points: 1,654, Level: 24
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Nov 2006
Location: India
Posts: 4
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: DNA Microarray analysis help please!

Hi,

Well when we talk about microarray data analysis it starts with normalization and can proceed till the biological interpretation. I am into the field of DNA data analysis and can even perform for you. There are several tutorials available on this topic. However, I believe that a good knowledge of statistics is required for the data analysis. As far as interpretation of DNA microarray data is concerned, I do not know what sort of experiment you are performing. Based on your experiment several other interpretation analysis can be performed besides GO based clustering and pathway analysis. If you need more information hesitate not to contact me.

Stanley
Reply With Quote
  #8  
Old 02-02-2007, 02:25 AM
cyberpostdoc's Avatar
Pipette Filler
Points: 1,509, Level: 23 Points: 1,509, Level: 23 Points: 1,509, Level: 23
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Feb 2007
Location: New Jersey
Posts: 21
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: DNA Microarray analysis help please!

R: open source statistics package.

Cyberpostdoc recommends R for statistics, biological data manipulations and graphics:

1. Describe basic statistics of your data.
2. Statistical tests can be done with simple, easy to understand commands.
3. Open source packages specific to microarray analysis.
4. R scripting language can further be used to program for more sophisticated tasks.
5. Example:
Data: Affymetrix microarray expression levels (HG-U95A) of seven genes inferred from the average difference values (AD), random picked from Su et al..
amygdala thalamus fetal brain whole brain caudate nucleus testis
gene1 32.47 39.17 32.33 29.37 44.65 84.59
gene2 54.51 64.76 40.52 31.26 50.92 45.76
gene3 12.14 8.78 3.59 5.43 7.22 48.67
gene4 65.95 5.49 28.54 109.90 83.06 304.02
gene5 34.61 43.86 36.54 35.67 36.44 27.65
gene6 134.53 147.83 133.96 33.89 130.17 216.44
gene7 62.09 25.48 52.20 67.65 44.14 122.73


Read the data in as tab-delimited file, gene names as rows, tissues as columns:
> as.matrix(read.table(file="p0002_data",sep="t",row .name=1,header=TRUE))->test.data


Boxplot shows that gene6 expression level is generally higher than others and that gene4 expression level varies the most across tissues; Pearson correlations of transcription profiles specified by genes can be used to cluster tissues:
> par(mfrow=c(1,2),mar=c(20,3,1,0)) // plot two image side by side
> boxplot(as.data.frame(t(test.data)),col=c(1:7),las =2) // boxplot at left
> plot(hclust(as.dist(1-cor(test.data,method="Pearson")),method="a"),xlab= "",main="") // cluster dendrogram at right, use Pearson correlation as distance, agglomeration method for clustering is "average"

Image


T-test show different in expression levels between gene5 and gene6:
> t.test(test.data["gene6",],test.data["gene5",])

Image

I am not allowed to paste image yet, so please go to my website and look into bioinformatics -> software review section.
Reply With Quote
  #9  
Old 02-03-2007, 06:37 AM
ecualchem's Avatar
Pipette Filler
Points: 1,521, Level: 23 Points: 1,521, Level: 23 Points: 1,521, Level: 23
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Dec 2006
Posts: 10
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: DNA Microarray analysis help please!

You can find a download book in the pages of embrace (seeks with google) click in the next and last courses choose the finland (I believe that it is) courses and choose books section and OK here you are your book.
Or (csc.fi/csc) +arraybook_overview Maybe go direct
Best regards
Ecualchem
Reply With Quote
  #10  
Old 02-13-2013, 02:38 PM
Pipette Filler
Points: 52, Level: 1 Points: 52, Level: 1 Points: 52, Level: 1
Activity: 0% Activity: 0% Activity: 0%
 
Join Date: Feb 2013
Posts: 1
Thanks: 0
Thanked 0 Times in 0 Posts
Default Re: DNA Microarray analysis help please!

Dear Stanley ,

I am doing some microarray analysis and I am very confused with some of the steps. Would you be able to provide me some advice on the same?

Thanks
Reply With Quote
Reply

Tags
analysis , dna , microarray


Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On

Forum Jump

Similar Threads
Thread Thread Starter Forum Replies Last Post
(control vs treatment) in (wildtype vs mutant) microarray analysis neokao Microarrays Forum 0 05-22-2009 06:12 AM
Control vs Treatment) in Wildtype vs Mutant Microarray analysis neokao Microarrays Forum 0 05-22-2009 05:57 AM
Free Microarray Software for Analysis moleculardude Microarrays Forum 2 03-06-2009 09:55 PM
Time Series microarray data analysis and loop design ali_22 Microarrays Forum 1 05-06-2008 02:32 PM
Microarray Data Analysis Software - Free Public Domain moleculardude Microarrays Forum 0 06-11-2007 01:15 PM


All times are GMT. The time now is 01:42 AM.


Powered by vBulletin® Version 3.8.4
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Copyright 2005 - 2012 Molecular Station | All Rights Reserved
Page generated in 0.17418 seconds with 16 queries