This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Can maSigPro be used to find out differentially expressed genes from microarray data i.e. .CEL files.

Can I use maSigPro package for this. As I used maSigPro package and got this error. What is meaning of this error, should I change samething in this R-script.

If you have any idea then suggest me.

> edesign
        Time Replicate Control hypoxic
Array1     3         1       1       2
Array2     2         1       2       1
Array3     2         1       1       2
Array4     1         2       2       1
Array5     1         2       1       2
Array6     3         2       2       1
Array7     3         2       1       2
Array8     2         2       2       1
Array9     2         2       1       2
Array10    1         3       2       1
Array11    1         3       1       2
Array12    3         3       2       1
Array13    3         3       1       2
Array14    2         3       2       1
Array15    2         3       1       2
Array16    1         1       2       1
Array17    1         1       1       2
Array18    3         1       2       1

fit <- p.vector(eset, design, Q = 0.05, MT.adjust = "BH", min.obs = 20)
Error in dat[, as.character(rownames(dis))] : subscript out of bounds
masigpro
• 3,564 views • link
updated by Ram Ram • written by jaichandpatel2 • jaichandpatel2

1 answer

Would need to see more code and data to troubleshoot this properly.

However, it is important that the row names of your design matrix match the column names of exprs(eset). Those names are usually the names of the files with the raw array data, e.g. *.CEL.gz for Affymetrix. You can assign the row names of edesign using:

rownames(edesign) <- X

where is X is a character vector with the array file names.

• 0 views • link
written by Neilfws Neilfws

Hello,

Please let me know also If you got solution.

• 1 views • link
written by sbb • sbb

Log in to answer this question.

More posts like this