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jenniferlneary
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@jenniferlneary-11265
Last seen 8.2 years ago
Hello,
I am comparing two types of methylation pull-down experiments on the same 8 genetically identical rats. (4 treatment, 4 control). I employed MEDIPS for this comparison and I chose EdgeR and TMM normalization. All seems well but we noticed in the data that sometimes (rarely) normalization raises 0 counts to a value in the RMS and RPKM columns. Is this a result of the normalization method? Is it expected? Why does it happen? Is it related to having adjacent DMRs that haven't been merged? I feel that the data is sound, I'd just like to be able to explain this. Here is an example:
DMR Start position | DMR Stop position | S1 raw count | S2 raw count | S3 raw count | S4 raw count | M1 raw count | M2 raw count | M3 raw count | M4 raw count | S1 RMS normalized | S2 RMS normalized | S3 RMS normalized | S4 RMS normalized | M1 RMS normalized | M2 RMS normalized | M3 RMS normalized | M4 RMS normalized |
1105201 | 1105300 | 0 | 0 | 0 | 0 | 6 | 6 | 8 | 8 | 0.22 | 0 | 0 | 0 | 0.47 | 0.43 | 0.45 | 0.47 |
1105301 | 1105400 | 0 | 0 | 0 | 0 | 7 | 2 | 8 | 8 | 0.26 | 0 | 0 | 0 | 0.53 | 0.35 | 0.51 | 0.51 |
Thank you,
Jennifer