Hi.
On Wed, Dec 1, 2010 at 4:08 PM, kraman <kripa...@hotmail.com> wrote:
> Hi, I'm new to microarray analysis and aroma.affymetrix
> I'm trying to create a dynamic report, output using arrayexplorer but
> i'm getting this error:
>
> Warning messages:
> 1: In is.na(x) : is.na() applied to non-(list or vector) of type
> 'NULL'
> 2: In writeImages.SpatialReporter(reporter, arrays = arrays, aliases =
> aliases, :
> No color maps specified. Nothing to do.
> 3: In is.na(x) : is.na() applied to non-(list or vector) of type
> 'NULL'
Nothing to worry about. Everything should work as expected.
Those are *warnings* not *errors*. In R, there is a strict difference
between the two. Typically when you get an *error*, the R
function/script stops, whereas with a *warning* everything continues.
Compare:
> log("a")
Error in log("a") : Non-numeric argument to mathematical function
and
> log(-1)
[1] NaN
Warning message:
In log(-1) : NaNs produced
>
> I'm trying to analyze huex chips. This is a summary of my code thus
> far if it's of any help:
>
> cdf<-AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2")
>
> cs<-AffymetrixCelSet$byName("Control", chipType="HuEx-1_0-st-v2")
>
> qn<- QuantileNormalization(cs)
> csN <- process(qn)
>
> plm<- RmaPlm(csN)
> fit(plm)
> ces<- getChipEffectSet(plm)
>
> rs<-calculateResidualSet(plm)
> ae<-ArrayExplorer(rs)
> process(ae) ###this is where i see the error
So if this keeps running, which I think it did for you, because
normally warnings are only displayed when everything is finished.
Have a look at the directory ./reports/Control/<some tags>/ and you
should see a file ArrayExplorer.html. Look in its subdirectories and
you should see large PNG files containing the spatial plots. Open
that in Firefox(!). Alternatively, you could also try display(ae) if
your default browser is Firefox.
/Henrik
>
> Any suggestions would be greatly appreciated!!
> Thanks
>
> -K
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
