[BioC] HELP: MICROARRAYS

[Steve Lianoglou]

Also -- I just realized this (since I got a bounce back), but please
don't CC bioconductor-request at r-project.org in your emails. By
default, people reply to emails via reply-all, so we're all stuck
sending emails there too, if we're not careful enough to notice that
the "request" email address is in there.

Please just send your bioc questions to: bioconductor at r-project.org

Thanks,
-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