baySeq

[unidodo]

I installed the latest version 1.8.3 and followed the manual, got the following error:

replicates <- c("simA", "simA", "simA", "simA", "simA", "simB", "simB", "simB", "simB","simB")

Error in validObject(.Object) :
invalid class "countData" object: invalid object for slot "replicates" in class "countData": got class "character", should be or extend class "numeric"

But they are characters in the manual as well.

Anyone experienced it? Tia.

[sunkorner]

Can anyone please let me know why I am encountering this problem in baySeq. Thank you.

> CDP.NBML <- getPriors.NB(CD, samplesize = 1000, estimation = "QL", cl = cl) > CDPost.NBML@estProps
Finding priors...Error in quantile.default(nzSD, 1:sqnum/sqnum) :
missing values and NaN's not allowed if 'na.rm' is FALSE

[DunningL]

Also, if anyone else is using the programme what number of iterations and bootstraps are you using for your data set?

[DunningL]

The problem appears to be that the 'raw.data' object is of class 'data.frame' rather than class 'matrix'. If you try the following:

> raw.data <- as.matrix(raw.data)

before the command

> CD <- new("countData", data = raw.data, replicates = replicates,
+ libsizes = libsizes, groups = groups)

then this should succeed.

[DunningL]

I was wondering if anyone else gets the error:

Error in validObject(.Object) :
invalid class "countData" object: invalid object for slot "data" in class "countData": got class "data.frame", should be or extend class "matrix"

when trying to import data into baySeq. I am using a simlar spreadsheet which worked for DESeq, DEGseq and edgeR but it doesnt work for baySeq. I have tried playing around with removing the labels etc but to no avail.

any help would be greatly appreciated