[BioC] HELP: MICROARRAYS

[Steve Lianoglou]

Hi,

As Marco has already mentioned: it's not clear what software you are using.

It seems as if you have a rather straightforward experimental design
(testing differential expression between two conditions, each of which
has several replicates).

Since you posted on the bioconductor mailing list, I'm going to assume
that you want to use bioconductor tools to solve your problem.

If I were you, I'd use limma:

http://www.bioconductor.org/packages/release/bioc/html/limma.html

Read through the user guide:
http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf

Pay attention to the case study section. You'll likely find something
quite similar to your setup in there.

Also:

DON'T TYPE IN CAPS, IT WILL MORE LIKELY ANGER PEOPLE THAN ENCOURAGE
THEM TO HELP YOU BECAUSE YOU ARE COMING OFF AS DEMANDING SOMETHING,
EVEN THOUGH YOU PROBABLY DON'T INTEND TO.

Good luck,

-steve


On Fri, Feb 25, 2011 at 5:49 AM, Poonam ** <vpoonam89 at gmail.com> wrote:
> "I am facing a problem in microarray gene expression analysis. I have
> uploaded a simple normalized text data file (i.e. of just 1.5Mb),
> Here is the sample of my dataset used.
>
>       Dis1    Dis2    Dis3    Dis4    Nor1    Nor2    Nor3
> Gene1   0       0.087   0       0       0       0       0.157
> Gene2   1.847   0.74    1.571   1.346   0.339   0.6     0.996
> Gene3   0.041   0.161   1.338   0.293   0       0.553   0.122
> Gene4   17.542  12.585  10.273  10.927  6.128   12.842  12.663
> Gene5   0.332   0.038   0.347   0.091   0.064   0       0.233
> Gene6   0.975   0.333   0.34    0.711   0.497   0.446   0.557
>
>
>  as my data is already is normalized one thus straightaway I wish to simply
> apply t-statistics, when i clicked on "T-statistics" section and in order to
> find differentially expressed genes I have opted two classes in one dataset,
> and set p value as 0.05 and for correction Benjamin-Hochberg.
>
>
> But instead of displaying result it shows the following error.
> R: Loading required package: tools
> Welcome to Bioconductor
> Vignettes contain introductory material. To view, type
> 'openVignette()' or start with 'help(Biobase)'. For details
> on reading vignettes, see the openVignette help page.
> Hmisc library by Frank E Harrell Jr
> Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
> to see overall documentation.
> NOTE:Hmisc no longer redefines [.factor to drop unused levels when
> subsetting. To get the old behavior of Hmisc type dropUnusedLevels().
> Attaching package: 'Hmisc'
> The following object(s) are masked from package:Biobase :
> contents
> Error in plot.window(xlim, ylim, log, asp, ...) :
> need finite 'xlim' values
>
>
> KINDLY HELP ME TO SOLVE THE ISSUE. I WILL BE VERY GREATFUL TO YOU
> THANKYOU"
>
>        [[alternative HTML version deleted]]
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact