On Wed, Jun 27, 2012 at 7:26 AM, thileepan sekaran <dena.dinesh@gmail.com>wrote:

> Hello Mr.Sean Davis,
>
>                               Thank you so much for timely guidance.I m
> new to R.Next time I will post with session info information.I tried using
> getGEO comannd but it gives an error of                 "Error in file(con,
> "r") : cannot open the connection".
>
> Session Info() :
>
> R version 2.12.2 (2011-02-25)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] GEOquery_2.17.5                      ArrayTools_1.10.0
>      mogene10sttranscriptcluster.db_6.0.1 org.Mm.eg.db_2.4.6
>
>  [5] RSQLite_0.10.0                       DBI_0.2-5
>      AnnotationDbi_1.12.1                 AffyExpress_1.16.0
>
>  [9] limma_3.6.9                          mogene10stv1cdf_2.7.0
>      affy_1.28.1                          vsn_3.18.0
>
> [13] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.18.0         grid_2.12.2           lattice_0.19-17
> preprocessCore_1.12.0 RCurl_1.5-0.1         tools_2.12.2
>  XML_3.2-0.2
> [8] xtable_1.6-0
>
>
>  As I m new to R,your help would be really useful.
>
> Regards
>
> Thileepan
>
>
>
Hi, Thileepan.  Please keep replies on the list.  You'll get the best help
that way.

I hate to do this to you, but your R version is about 3 years old, so I
suggest as a first step to update R to the current version and try again.
 We don't attempt to maintain software that old.  If you have problems,
please again post sessionInfo(), the code you used (cut-and-paste) and the
output/error.

Sean




>
>
> On Wed, Jun 27, 2012 at 12:40 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
>>
>>
>> On Wed, Jun 27, 2012 at 6:19 AM, Thileepan [guest] <
>> guest@bioconductor.org> wrote:
>>
>>>
>>>    I m Thileepan Sekaran Pursuing my Masters in Bioinformatics.
>>> Currently I m doing the gene expression profiling of affymetrix data in R.
>>> I found the affyexpress package from Bioconductor very interesting and want
>>> to use for my analysis but i was stuck when I wanted to find out the
>>> differential expressed genes using AffyRegress. The dataset GSE37859 which
>>> has been generated in MoGene-1_0-st platform  consist of two groups
>>> Fibroblast and iNSC cells and I wanted to find the differentially expressed
>>> genes between these two groups with fold change of 2 and pvalue of .05.Can
>>> any one help me in finding the differantial expressed genes for the dataset
>>> btween two groups.
>>>
>>>
>> Hello, Thileepan.
>>
>>
>>>  -- output of sessionInfo():
>>>
>>>
>> The output of sessionInfo() should be included in your email.  You can
>> get that by pasting in the output after typing "sessionInfo()" into your R
>> session after your error occurs.
>>
>>
>>> "Error in function (classes, fdef, mtable)  :
>>>  unable to find an inherited method for function "annotation", for
>>> signature "matrix"
>>>
>>>
>> You'll need to send us some code that lets us know how you came to the
>> error.
>>
>> To answer your question directly, though, I'd suggest using the GEOquery
>> package to generate an ExpressionSet for your GSE and then use limma for
>> calculating differential expression.
>>
>> > library(GEOquery)
>> > gse = getGEO("GSE37859")[[1]]
>>
>> I think you'll find your annotation of interest here:
>>
>> > cell_type = pData(gse)$characteristics_ch1
>> > levels(cell_type)
>> [1] "cell type: induced neural stem cell"
>> [2] "cell type: mouse embryonic fibroblast"
>> [3] "cell type: neural stem cell"
>>
>> If we want to change the levels of the factor, that is possible.
>>
>> > levels(cell_type) = c('iNSC','MEF','NSC')
>> > cell_type
>>   V2   V3   V4   V5   V6   V7   V8   V9  V10  V11  V12  V13
>> iNSC iNSC iNSC iNSC iNSC iNSC  NSC  NSC  NSC  MEF  MEF  MEF
>>
>> You can use that column to design your design matrix in limma.
>>
>> > library(limma)
>> > dm = model.matrix(~ 0 + cell_type)
>> > dm
>>    cell_typeiNSC cell_typeMEF cell_typeNSC
>> 1              1            0            0
>> 2              1            0            0
>> 3              1            0            0
>> 4              1            0            0
>> 5              1            0            0
>> 6              1            0            0
>> 7              0            0            1
>> 8              0            0            1
>> 9              0            0            1
>> 10             0            1            0
>> 11             0            1            0
>> 12             0            1            0
>> attr(,"assign")
>> [1] 1 1 1
>> attr(,"contrasts")
>> attr(,"contrasts")$cell_type
>> [1] "contr.treatment"
>>
>> From here, you should be able to follow along in the limma manual.
>>
>> Hope that helps,
>>
>> Sean
>>
>>
>

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