Hello Everyone,
I have RNAseq data set which I looked at the expression profile of a wild-type and gene knockout mutant at two pHs (7.4 and 5.0). I want to identify modules that are associated with pH and genetic background. So for the trait files, I used binary values (0,1) to indicate whether it is that pH and genetic background, for example: pH7.4-WT.
The trait files looks like this:
Sample pH5.0_WT pH5.0_mut pH7.4_WT pH7.4_mut
pH5.0_WT_rep1 1 0 0 0
pH5.0_WT_rep2 1 0 0 0
pH5.0_WT_rep3 1 0 0 0
pH5.0_mt_rep1 0 1 0 0
pH5.0_mt_rep2 0 1 0 0
pH5.0_mt_rep3 0 1 0 0
pH7.4_WT_rep1 0 0 1 0
pH7.4_WT_rep2 0 0 1 0
pH7.4_WT_rep3 0 0 1 0
pH7.4_mt_rep1 0 0 0 1
pH7.4_mt_rep2 0 0 0 1
pH7.4_mt_rep3 0 0 0 1
By doing this, I got the module-trait graphs which has 4 columns corresponding to the 4 traits. Below:
Is this the correct way to do it? because I don't actually have a quantitative trait.
(Just learnt that the it is recommended to have more at 20 replicates (which I don't have at all), and I suppose the average of these replicates were used instead of like this).
Thank you!
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heyang •
1 answer
Well, at least you have different statistically significant correlations for each group, but what do they mean (?) - take a look at the genes behind each statistically significant module and see if you can infer anything from them.
Keep in mind the following:
- there are many different ways that you can approach your analysis, given the data that you have
- WGCNA will not conclusively give you a result for your study - at best, it may simply guide you. Be conscious of 'cherry picking' results that you want to find
Kevin
Hey, do you mean either of these:
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Please use the formatting bar (especially the
codeoption) to present your post better. You can use backticks for inline code (`text` becomestext), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.Also, tabular data can be displayed much more elegantly when the
columncommand is used well.Surely you mean WGCNA? Shouldn't that be a tag so the question pops up on a tag based search?
Thanks for the advice, did change it.