[BioC] R: HELP: MICROARRAYS

[Manca Marco (PATH)]

Dear Poonam,

first of all might I invite you to read the posting guide here? -> http://www.bioconductor.org/help/mailing-list/posting-guide/

Might I also remind you that is commonly accepted netiquette not to use afinalistic text capitalization in a message, as it is equivalent to screaming to try to catch someone's attention in real world?

That said, I am not sure what kind of software environment are you working on when you mention << i clicked on "T-statistics" section>>.

Could you give us some background on the installation of R/Bioconductor you are working on? On which OS? Could you copy and paste the code you are using, either by writing it yourself or by mean of an intermediate interface, and the results of your sessionInfo() and traceback()?

If you are using a proprietary software which is in turn summoning R, maybe it could be relevant to contact their assistance service.

All the best, Marco


--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)

Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX Maastricht

E-mail: m.manca at maastrichtuniversity.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka


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________________________________________
Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Poonam ** [vpoonam89 at gmail.com]
Inviato: venerdì 25 febbraio 2011 11.49
A: bioconductor-request at r-project.org; bioconductor at r-project.org
Oggetto: [BioC] HELP: MICROARRAYS

"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"

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