Add classes or separate cases by disease status

Question

[ab123]

Hi there,

I'm trying to separate the data sets here into different classes or assign class tags (in this case: AD, MC, Control). However, I'm not sure how to tackle this other than manually, which is a bit of a drag at 700 samples.

The problem is that the data sets aren't organised. The classes are missing and when checking the data, they are all lumped together so an AD case follows a control etc.

If there's no work around I will of course do this manually, but if someone knows a way to assign classes from some of the info files, I'd be grateful to know or be pointed in the right direction.

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-63060/?keywords=alzheimers&organism=Homo+sapiens&exptype%5B%5D=&exptype%5B%5D=&array=

http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-63061/?keywords=alzheimers&organism=Homo+sapiens&exptype%5B%5D=&exptype%5B%5D=&array=

Answer 1

[Lars Juhl Jensen]

If you look in the .sdrf.txt files for the two studies, you will find a column called Characteristics [status]. For each sample it has a value, which is either AD, MCI, or CTL. I assume these refer to Alzheimer's Disease, Mild Cognitive Impairment, and Control, respectively.

[ab123]

Hi Lars, yes, but how is that assigned or used in R? Looking at the file it still doesn't match the data file. The values for each sample aren't in the same order as those in the actual data file. Is there a way to auto assign these to the expression data set in R? Thank you!

[Lars Juhl Jensen]

Sorry, can't help you with that. I don't do R.