SAM r for finding up and down regulated genes
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Linda Chaba ▴ 10
@linda-chaba-9480
Last seen 3.5 years ago
Kenya

I'm using the below code for samr to find down and up regulated genes


source("http://bioconductor.org/biocLite.R")

biocLite(samr)

data=celline.data #expression data imported from excel file whose columns are samples and rows are genes. First row has quantitative outcome.
x=data[-1,] #expression data only without quantitative outcome
y=data[1,] #Quantitative outcome

library(samr)

sam.data<-list(x=x,y=y, geneid= 1:nrow(data), genenames= row.names(data))  # prepare the data list required in “samr” #function
samr.obj<-samr(sam.data,  resp.type="Quantitative", nperms=100, random.seed=12345) 

The last line is producing this error 

Error in storage.mode(x) <- "double" : 
  (list) object cannot be coerced to type 'double'
In addition: Warning message:
In knnimp(x, k, maxmiss = rowmax, maxp = maxp) :
  2950 rows with more than 50 % entries missing;
 mean imputation used for these rows
Error during wrapup: cannot open the connection


I'll appreciate if someone can point out for me what I'm not doing right.

Thank you.

samr • 1.4k views
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@valerie-obenchain-4275
Last seen 11 months ago
United States

samr is not a Bioconductor package so the authors probably aren't watching this mailing list. For help with CRAN packages it's better to post to the R-help mailing list

https://www.r-project.org/mail.html

Valerie

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Entering edit mode

Thank you Valerie for pointing that out.

 

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