Can maSigPro be used to find out differentially expressed genes from microarray data i.e. .CEL files.

Question

[jaichandpatel2]

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

Answer 1

[Neilfws]

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.

[jaichandpatel2]

You mean to say that rownames should be same as names of .CEL files.

I have done the same but did not get any improvement in output.

I have taken E-GEOD-35819 dataset from http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-35819/samples/

I have some more datasets like this

Please help if you can ...

[sbb]

Hello,

Please let me know also If you got solution.