How to use SamR
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aristotele_m ▴ 30
@aristotele_m-6821
Last seen 4.4 years ago
Italy

Dear All,

I want to use samr on my rnaseq data.

After  I prepare my normalizate expression value using deseq2 I want to use  samr for detect whihc is the  gene responbile for the difference from on set of data to another.


Dati.coun <- counts(dds,normalize=TRUE)

colnames(Dati.coun)[match(colnames(Dati.coun)[id],colnames(Dati.coun))] <-1
colnames(Dati.coun)[(colnames(Dati.coun) != "1")] <-2

head(Dati.coun,3)
                         1         1          1        2         2          1         2
ENSG00000000003 195.080779 27.020672 111.743404 86.11620 55.208979 100.766001 76.288760
ENSG00000000005   4.150655  1.501148   2.793585  4.30581  1.648029   3.148938  4.146128
ENSG00000000419  70.561133 59.295364  48.887739 47.36391 59.329052  89.315319 60.533473

sam.data<-list(x=Dati.coun,y=colnames(Dati.coun), geneid= 1:nrow(Dati.coun), genenames=rownames(Dati.coun), logged2=T) 

samr.obj<-samr(sam.data,  resp.type="Two class unpaired", nperms=100, random.seed=12345) ##

Error in ttstar[, j] <- -1 * sort(-1 * ttstar[, j]) :
  replacement has length zero
In addition: There were 50 or more warnings (use warnings() to see the first 50)

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pamr_1.55                 survival_2.37-7           cluster_1.15.3           
 [4] DESeq2_1.4.5              RcppArmadillo_0.4.450.1.0 Rcpp_0.11.3              
 [7] GenomicRanges_1.14.4      XVector_0.2.0             IRanges_1.20.7           
[10] ALL_1.4.16                Biobase_2.22.0            BiocGenerics_0.8.0       
[13] BiocInstaller_1.12.1      samr_2.0                  matrixStats_0.10.0       
[16] impute_1.36.0            

loaded via a namespace (and not attached):
 [1] annotate_1.40.1      AnnotationDbi_1.24.0 DBI_0.3.1            digest_0.6.4        
 [5] genefilter_1.44.0    geneplotter_1.40.0   grid_3.1.1           htmltools_0.2.6     
 [9] lattice_0.20-29      locfit_1.5-9.1       RColorBrewer_1.0-5   rmarkdown_0.3.3     
[13] R.methodsS3_1.6.1    RSQLite_0.11.4       stats4_3.1.1         tools_3.1.1         
[17] XML_3.98-1.1         xtable_1.7-4         yaml_2.1.13 

 

Could you help me on resolve this isssue?

thanks in advance for any help!

 

samr rnaseq CRAN • 1.9k views
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1
Entering edit mode
aristotele_m ▴ 30
@aristotele_m-6821
Last seen 4.4 years ago
Italy

I resolve I need only to delete 0 on the rows

 

row_sun<-apply(Dati.coun, 1, function(row) all(row !=0 ))
Da<-Dati.coun[row_sun,]
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