Question

To convert MAList to ExpressionSet using R package 'convert'

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rheupion • 0

@rheupion-11829

Last seen 8.2 years ago

I'm currently working on a meta-analysis of transcriptomics datasets that have published recently.

I want to convert MAList to ExpressionSet using R package 'convert'.

However, I had an error message as following.

> eSet <- as(MA, "ExpressionSet")

Error in `rownames<-`(`*tmp*`, value = c("10A_12477149", "10B_12477150", :

attempt to set 'rownames' on an object with no dimensions

I don't know what the message indicates and how to settle this problem.

convert • 1.6k views

ADD COMMENT • link updated 8.2 years ago by Gordon Smyth 52k • written 8.2 years ago by rheupion • 0

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Why do you want to convert an MAList to ExpressionSet? Can you not use the MAList for whatever you are doing?

ADD REPLY • link 8.2 years ago James W. MacDonald 68k

score 0 · Answer 1 · 2016-11-11

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rheupion • 0

@rheupion-11829

Last seen 8.2 years ago

I've just resolved the problem.

The 'targets' format in the MAList file was omitted.

After adding the 'targets', the function 'as' worked.

Thank you.

ADD COMMENT • link 8.2 years ago rheupion • 0

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Yes, that's a resolution. MA$targets is an optional component of an MAList object, but the authors of the MAList to ExpressionSet method in the convert package have assumed that it always exists. More robust code would check whether MA$targets was NULL.

Also be aware that the conversion of an MAList to an ExpressionSet is only valid if the two-color microarray experiment used a common reference for all microarrays. In that case, the conversion to an Expression set basically just extracts the matrix MA$M, in which case you could just work with MA$M yourself.

ADD REPLY • link 8.2 years ago Gordon Smyth 52k