Thanks Sean. I already used limma for my analyses. I was just trying to repeat the data analysis used in the original paper (GSE121). But I have an idea on how to proceed now. Thanks again. -Avoks On Tue, Mar 20, 2012 at 2:46 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > > > On Tue, Mar 20, 2012 at 8:37 AM, Ovokeraye Achinike-Oduaran > <ovokeraye at="" gmail.com=""> wrote: >> >> Hi, >> >> Sorry about the vagueness. >> >> This is how I have retrieved my data from GEO. I'm trying to see the >> DE of the genes across the two conditions (IR and IS). I just couldn't >> figure out how to apply this info to wilcox.test() >> >> gds157dat = getGEO('GDS157',destdir=".") >> gds157eset = GDS2eSet(gds157dat, do.log2=TRUE) >> groups= pData(gds157eset)$metabolism >> groups=as.character(groups) >> groups[groups=="insulin sensitive"]= "IS" >> groups[groups=="insulin resistant"]= "IR" >> > > First, wilcox.test works on a gene/probe at a time, so you'll need some type > of looping structure (apply, for example). ?Second, you'll need to split > your data into two vectors corresponding to the IR and IS subsets; these two > vectors will be the x and y variables in wilcox.test. > > You might also look at the multtest package and consider using limma. > ?Particularly since your data contain only 10 samples, rank-based methods > are going to be of limited use. > > Sean > > > > >> >> sessionInfo() >> R version 2.14.1 (2011-12-22) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_.1252 ?LC_CTYPE=English_.1252 >> [3] LC_MONETARY=English_.1252 LC_NUMERIC=C >> [5] LC_TIME=English_.1252 >> >> attached base packages: >> [1] stats4 ? ?splines ? stats ? ? graphics ?grDevices utils ? ? datasets >> [8] methods ? base >> >> other attached packages: >> ?[1] coin_1.0-21 ? ? ? ? modeltools_0.2-19 ? mvtnorm_0.9-9992 >> ?[4] survival_2.36-12 ? ?XML_3.9-4.1 ? ? ? ? RCurl_1.91-1.1 >> ?[7] bitops_1.0-4.1 ? ? ?puma_2.6.0 ? ? ? ? ?mclust_3.4.11 >> [10] limma_3.10.2 ? ? ? ?ArrayExpress_1.14.0 affy_1.32.1 >> [13] GEOquery_2.20.8 ? ? Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.22.0 ? ? ? ? BiocInstaller_1.2.1 ? preprocessCore_1.16.0 >> [4] zlibbioc_1.0.0 >> > >> >> Regards, >> >> Avoks >> >> On Tue, Mar 20, 2012 at 2:15 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> > >> > >> > On Tue, Mar 20, 2012 at 7:56 AM, Vincent Carey >> > <stvjc at="" channing.harvard.edu=""> >> > wrote: >> >> >> >> Please read the posting guide >> >> http://www.bioconductor.org/help/mailing-list/posting-guide/ before >> >> >> querying this list. >> >> >> >> You have not given any information on how you have used getGEO. ?To >> >> help >> >> you, I issued >> >> >> >> > library(GEOquery) >> >> Setting options('download.file.method.GEOquery'='auto') >> >> >> > gg = getGEO("GDS157") >> >> File stored at: >> >> >> >> >> >> /var/folders/4D/4DI98FkjGzq0K2niUTEHSE+++TM/-Tmp-//RtmpGnz9Cf/GD S157.soft.gz >> >> > gg >> >> An object of class "GDS" >> > >> > >> > At this point, if you would like to work with an ExpressionSet instead >> > of a >> > GDS object, try: >> > >> > expset = GDS2eSet(gg) >> > >> > Sean >> > >> >> >> >> channel_count >> >> [1] "1" >> >> dataset_id >> >> [1] "GDS157" "GDS157" >> >> description >> >> [1] "Analysis of gene expression in pooled vastus lateralis muscle >> >> samples >> >> from insulin-sensitive and insulin-resistant equally obese, >> >> non-diabetic >> >> Pima Indians. A search for susceptibility genes for type 2 diabetes. >> >> ?" >> >> ... >> >> >> >> > getClass("GDS") >> >> Class "GDS" [package "GEOquery"] >> >> >> >> Slots: >> >> >> >> Name: ? ? ? ? ? gpl ? ?dataTable ? ? ? header >> >> Class: ? ? ? ? ?GPL GEODataTable ? ? ? ? list >> >> >> >> Extends: "GEOData" >> >> > getClass("GEODataTable") >> >> Class "GEODataTable" [package "GEOquery"] >> >> >> >> Slots: >> >> >> >> Name: ? ? columns ? ? ?table >> >> Class: data.frame data.frame >> >> >> >> Here I am using R's self-describing capacities to learn about what the >> >> query returned. >> >> >> >> > gg at dataTable@columns >> >> ? ?sample ? ? ? ?metabolism >> >> 1 ?GSM2289 insulin resistant >> >> 2 ?GSM2294 insulin resistant >> >> 3 ?GSM2299 insulin resistant >> >> 4 ?GSM2304 insulin resistant >> >> 5 ?GSM2309 insulin resistant >> >> 6 ?GSM2313 insulin sensitive >> >> 7 ?GSM2318 insulin sensitive >> >> 8 ?GSM2323 insulin sensitive >> >> 9 ?GSM2328 insulin sensitive >> >> 10 GSM2333 insulin sensitive >> >> >> >> description >> >> 1 ?Value for GSM2289: insulin resistant sample pool 1 muscle on HuFL; >> >> src: >> >> muscle >> >> 2 ?Value for GSM2294: insulin resistant sample pool 2 muscle on HuFL; >> >> src: >> >> muscle >> >> 3 ?Value for GSM2299: insulin resistant sample pool 3 muscle on HuFL; >> >> src: >> >> muscle >> >> 4 ?Value for GSM2304: insulin resistant sample pool 4 muscle on HuFL; >> >> src: >> >> muscle >> >> 5 ?Value for GSM2309: insulin resistant sample pool 5 muscle on HuFL; >> >> src: >> >> muscle >> >> 6 ?Value for GSM2313: insulin sensitive sample pool 1 muscle on HuFL; >> >> src: >> >> muscle >> >> 7 ?Value for GSM2318: insulin sensitive sample pool 2 muscle on HuFL; >> >> src: >> >> muscle >> >> 8 ?Value for GSM2323: insulin sensitive sample pool 3 muscle on HuFL; >> >> src: >> >> muscle >> >> 9 ?Value for GSM2328: insulin sensitive sample pool 4 muscle on HuFL; >> >> src: >> >> muscle >> >> 10 Value for GSM2333: insulin sensitive sample pool 5 muscle on HuFL; >> >> src: >> >> muscle >> >> >> >> Now I start to see that the collection of samples may be viewed as >> >> falling >> >> into two classes. ?If you want to use wilcox.test to address a >> >> two-sample >> >> problem arising from this experiment, you will have to use the >> >> information >> >> shown above to distinguish numerical values on gene expression into the >> >> classes. ?There is more than enough information in the above to begin >> >> this >> >> process; for biological interpretation you need to know a little more: >> >> you >> >> will need to know the GPL80 is documented in the package hu6800.db. >> >> >> >> On Tue, Mar 20, 2012 at 7:24 AM, Ovokeraye Achinike-Oduaran < >> >> ovokeraye at gmail.com> wrote: >> >> >> >> > Hi all, >> >> > >> >> > I am not quite sure how to use the expression set I get from >> >> > getGEO(), >> >> > say gds157, in wilcox.test(). >> >> > >> >> > Please help. >> >> > >> >> > Thanks. >> >> > >> >> > Avoks >> >> > >> >> > _______________________________________________ >> >> > Bioconductor mailing list >> >> > Bioconductor at r-project.org >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> > Search the archives: >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > >> >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> >> >> >> >> _______________________________________________ >> >> Bioconductor mailing list >> >> Bioconductor at r-project.org >> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Search the archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >