Question: Heatmap with just two columns
0
gravatar for Mozart
5 months ago by
Mozart240
Mozart240 wrote:

Hello everyone, I have been asked to summarise information from my count matrix - obtained from 4 replicates - in just two columns (one column per group). What's the best approach to do this? I usually use the following steps to get a classical heatmap containing as many tiles as per replicate

top <- head(order(-rowVars(assay(rld))),100)

and then I take out the row mean

mat <- assay(rld)[ top, ]
mat <- mat - rowMeans(mat)

Once I got what I want I use heatmap.2 to plot my results.

Since I have already applied the mean centring here, if I wanted to present my data as just two separate columns (thus merging values from each replicate in just one tile/condition), I should take the average from each group (i.e. condition 1 and condition 2); in this way I always get almost 'specular' results and I don't think it is correct to do this way. Any ideas?

heatmap rna-seq • 202 views
ADD COMMENTlink written 5 months ago by Mozart240
1
gravatar for ATpoint
5 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

Z-scaling with only two columns is not very informative imho since you will see only a bimodal high and low pattern. Why don't you do it like everyone does, so perform standard DE analysis, take the differential genes and then show a heatmap for those genes based on the Z-score for all samples.

ADD COMMENTlink modified 5 months ago • written 5 months ago by ATpoint40k

Thanks so much for your reply. Sometimes it is hard to change someone else's mind, if you know what I mean! It's all about being persuasive and kind at the same time but it's just hard sometimes. But thanks a lot, I do appreciate the fact that the common way of doing this is actually the usual approach I use..

ADD REPLYlink written 5 months ago by Mozart240
1

I have the experience that PIs can be easily persuaded with nice figures rather than words. Show them a proper alternative and things will be ok ;-)

ADD REPLYlink written 5 months ago by ATpoint40k

Thanks a lot!! I will do!

ADD REPLYlink written 5 months ago by Mozart240
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 925 users visited in the last hour