Log2 fold change heatmap

Question

[EVR]

Hi,

I have microarray data set where two conditions (Control versus KD) were compared. I want to have generate a heatmap which depicts the log2 fold change for subset of genes. As my result table reflects the Log2_foldchanges of KD samples,in order to find the corresponding log2_foldchanges in Control samples, I multiplied the log2_foldchanges in KD samples by -1 and generated the heatmap out of it. For an example

              Control_log2FC                       KD_log2FC
Gene_A        -2.3                                 2.3
Gene_B         1.7                                -1.7
Gene_C         4.2                                -4.2

Is my approach to generate the log2_foldchange heatmap is right?

Any help would be appreciated.

Thanks in advance.

Regards
Dino

Answer 1

[Devon Ryan]

Well, the log2FC is, by definition, a fold change between groups, so KD_log2FC contains both KD and control samples. But yes, if you want control to be the numerator then you just change the sign,

[EVR]

Thank you Devon. I hope the heatmap I generated with between control_log2Foldchange(changing the sing) and KD_log2foldchange(without changing sign) makes sense. Thank you once again for your guidance

Answer 2

[Alternative]

For me, it doesn't make sense. You will be duplicating the information in the heatmap with two columns showing the same information.

[Devon Ryan]

Yeah, I'm rather hoping that Dino doesn't think the fold-changes represent individual groups.