Mathjax: how to deal with this strange behavior?

Question

I am using the markdown editor and I have loaded Mathjax in all pages of my website.

I have realized that this line of latex works well:

$(u_1)$

However, this one does not work (basically latex does not work):

$(u_1,u_2)$

In order to make this work, I have to write something like this:

$(u\_1,u\_2)$

I have a similar problem here. This does not work:

$$M=\left(\begin{array}{cc}
a & b \\
c & d \\
\end{array}\right)$$

But this works:

$$M=\left(\begin{array}{cc}
a & b \\\\
c & d \\\\
\end{array}\right)$$

Answer 1

This is a common issue of mixing LaTeX-input with Markdown. From the MathJax documentation:

There cannot be HTML tags within the math delimiters (other than <br>) as TeX-formatted math does not include HTML tags.

And later:

Another source of difficulty is when MathJax is used in content management systems that have their own document processing commands that are interpreted before the HTML page is created. For example, many blogs and wikis use formats like Markdown to allow you to create the content of you pages. In Markdown, the underscore is used to indicate italics, and this usage will conflict with MathJax’s use of the underscore to indicate a subscript. Since Markdown is applied to the page first, it will convert your subscripts markers into italics (inserting tags into your mathematics, which will cause MathJax to ignore the math).

As other answers on SO (see the link at the top) point out, some markdown parsers are more aware of TeX-like syntax than others.