Hello Everyone,
I was having a look at TCGA 450K data and I downloaded also the data at two levels, ie., level 2 and level3.
Level 2, looks like this:
Composite Element REF Methylated_Intensity Unmethylated_Intensity Detection_P_value
cg00000029 2488.00579881129 2281.3142892634 0
cg00000108 8943.62421381116 336.745081332759 0
cg00000109 3827.0493383932 219.47270455192 0
cg00000165 263.820225926362 2355.4623873349 0
cg00000236 3733.92206994152 722.124674419151 0
cg00000289 1503.38837282518 277.513187258243 0
cg00000292 9650.668135454 1618.68980927383 0
cg00000321 5918.34421148769 4384.53097589033 0
while level 3, looks like this:
Composite Element REF Beta_value Gene_Symbol Chromosome Genomic_Coordinate
cg00000029 0.521668865344633 RBL2 16 53468112
cg00000108 NA C3orf35 3 37459206
cg00000109 NA FNDC3B 3 171916037
cg00000165 0.100722321673368 1 91194674
cg00000236 0.837944995677383 VDAC3 8 42263294
cg00000289 0.844172640712807 ACTN1 14 69341139
cg00000292 0.856363617411664 ATP2A1 16 28890100
cg00000321 0.574436174742582 SFRP1 8 41167802
Anyone, who has used this data can please tell me how I can Identify the regions/genes that are hyper and hypo-methylated.
Thank you
What you have downloaded are per-sample files describing the methylation values at single CG sites. Hyper- and hypo-methylation are "relative" terms, so you will need to define two (or more) groups and then look for differential methylation.
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written
by
Sean Davis
Hi Sean,
Thank you for your answer but I have another one for example say I have another group of values for second sample and I have to compare them and then identify regions that are hyper or hypo methylated? then which level of data shall I use (level2 or level 3) and how can I use it ? and secondly is it possible to use 3 Vs 13 samples to identify hyper and hypomethylated regions.
Thank you
You can use the level3 data, and compare the beta values between 2 or more groups. Logit transformation to M values will help with the statistical analysis.
You can also summarize multiple probes annotated to the same CpG island to a single value (e.g. mean) and compare the difference at the island level. Also M value will be helpful in comparison.
3 vs. 13 is OK.
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written
by
jianggl2000 •
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