Dear all,

I would be very grateful for some desperately needed help.

I am trying to run backgroundCorrect command in R after I loade the limma package.  However, I came up with an error code saying: Could not find function "backgroundCorrect"

I am sure that I have installed the limma packages and the statmod.

Any help will be much appreciated

Regards

Dominic Leung

Dear Dominic,

I am guessing, since you say that you're not sure how to type sessionInfo() at the R prompt, that this may be one of the first times that you are running R.

You have to understand that, so far, you're not giving us much information to help you. First you said that the error message was 'Could not find function "backgroundCorrect"'. You could only get this message if you have not in fact loaded limma. From your comments to Efstathios, I guess you later realized that you have to type library(limma) before you can start using limma functions.

Then you said that you got the error message 'Array 1Error in (1 - h) * qs[i] : non-numeric argument to binary operator'.

It is hard to diagnose problems without knowing what commands you have used. Usually people who ask for help have to show all the R code that they have run up to the point that they get the first error message. People also need to show us the output from typing

sessionInfo()

at the R prompt. Have a read of the posting guide at https://www.bioconductor.org/help/support/posting-guide/

I am going to take a wild stab and guess that you have not read the microarray expression data into R correctly. I am guessing that you have actually read a data.frame with columns of different types, and that you have tried to background correct data that is not actually numerical. I am guessing that you may have input a character matrix or some such to backgroundCorrect() instead of a numeric matrix. This could happen if you have read annotation and intensities as a data.frame, then left a column of annotation in when you intended to subset the intensities.

It would be a good idea for you to run your R code line by line and check that you are in fact inputting the correction quantities to each function.

Dear d.leung,

what kind of platform do you want to perform background ? Also could you provide your current sessionInfo() ? It seems weird to say that you have loaded the limma package and then the above error 

Best,

Efstathios