cing reads to microarray image files. There can even be different states of “raw” data, for example for a RNA-seq dataset you may have</p>
<ul>
<li>FASTQ files (raw reads)</li>
<li>BAM files (aligned reads)</li>
<li>gene by sample expression matrix (unnormalized)</li>
<li>gene by sample expression matrix (normalized)</li>
</ul>
<p>So what is “raw” and what is “processed” can be very context dependent.</p>
<p>In some cases there is a consensus in the field. For Affymetrix gene expression microarr