deletions | additions       diff --git a/methods-array.md b/methods-array.md  index 241944f..f4e9f0a 100644  --- a/methods-array.md  +++ b/methods-array.md 
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> Include how comparisons were made..  Samples were labeled using the NimbleGen Dual-Color DNA Labeling Kit and the arrays were processed according to the manufacturer’s recommendations (Roche NimbleGen, Madison, Wisconsin) and imaged at 5um using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA).  Raw data from both the Cy3 and Cy5 channels were ......... diff --git a/methods-rna2.md b/methods-rna2.md  index 7b39a0e..d1a6fc0 100644  --- a/methods-rna2.md  +++ b/methods-rna2.md 
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2) Next, open the **Reference Annotations** section and add a custom reference annotation file using the `merged_with_ref_ids.gtf` file from the cuffmerge output folder.   3) Click **Launch Analyses** and monitor the status of you job.  what the fork