Question: WGNCA (correlation network): how can I incorporate mutant and wildtype into the same network analysis?
0
gravatar for heyang
9 days ago by
heyang0
heyang0 wrote:

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: 11

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!

wgcna rna-seq R • 138 views
ADD COMMENTlink modified 9 days ago by Kevin Blighe41k • written 9 days ago by heyang0

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), 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.
code_formatting

Also, tabular data can be displayed much more elegantly when the column command is used well.

WGNCA

Surely you mean WGCNA? Shouldn't that be a tag so the question pops up on a tag based search?

ADD REPLYlink modified 9 days ago • written 9 days ago by RamRS21k

Thanks for the advice, did change it.

ADD REPLYlink written 9 days ago by heyang0
2
gravatar for Kevin Blighe
9 days ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k wrote:

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:

  1. there are many different ways that you can approach your analysis, given the data that you have
  2. WGCNA will absolutely never 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

If I had your data, I would honestly be doing other things such as regression modeling - WGCNA would be a final resort.. a bioinformatics equivalent of a 'Hail Mary' pass in the NFL.

Kevin

ADD COMMENTlink written 9 days ago by Kevin Blighe41k

"such as regression modeling" you had one post which showed regression modelling in biostar , can you provide the link ,i did look but couldn;t find it, as i couldn;t recollect the question you had answered for ..

ADD REPLYlink written 8 days ago by krushnach80480
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