Hello BIoconductor experts, I am a new user (first time posting!) and an
undergrad student at UC Berkeley, working with the NCI-60 cancer cDNA
microarray without bioconductor.  I only recently discovered bioconductor
and its abilities and would love to use it.  It seems that there are many
different packages out there, but I don't know which one might be helpful
(limma possibly?).  I just want to see the number of records with p-value
of, say, 10^-3 and possibly what gene that is attached to.  If you need more
information from me, please let me know.

 

If you want to know the details, here is the data set I used:

 

http://discover.nci.nih.gov/nature2000/data/selected_data/t_matrix9706_flags
.txt

 

filtered out entries with > 15 "NA" to reduce the rows from 9706 to 5911

 

then, using the latest version of R:

 

 

#NCI60 gene expression for spearman and p-value

 

nci60 <- as.matrix(read.table("c:/nci605911rows.txt", header = TRUE))

 

nci.cor <- cor.test(x = nci60[1, 2:61], y = nci60[2, 2:61], method =
"spearman")

 

writeLines(paste(nci.cor$estimate, nci.cor$p.value, sep=" "))

 

for(i in 1:(nrow(nci60) - 1))

 

{ 

     writeLines(paste("Row I", i, sep = " "))    

   for(j in (i+1):(nrow(nci60)))

   {

     writeLines(paste("Row J", j, sep = " "))    

     nci.cor <- cor.test(x = nci60[i, 2:61], y = nci60[j, 2:61], method =
"spearman");

     writeLines(paste(nci.cor$estimate, nci.cor$p.value, sep=" "))

    }

}

 

To generate these results:

 

Row  1                

Row  2                

0.0473    0.7258

Row  3                

0.2431 0.0710

.

(etc.)

.

Row  5911         

0.0055    0.9677

Row 2

Row 3

0.0034    0.4543

 

Where Row = unique gene, First number= spearman, followed by p-value

 

But here it gets tricky since working with this data does not tie back
easily with the genes.  I hope that maybe a bioconductor package can
streamline this.  

 

Thanking you all in advance,

 

John

 


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