0 comment Wednesday, May 14, 2014 | admin
I think I got home after 10pm last night...not exactly sure. I am sure that I spent nearly 12 hours processing samples from crummy data set yesterday...and I am not yet finished.I really hate this data set for the following reasons:It took me 8 months to generate these samples which is stupidly long considering what they are, but for reasons entirely outside of my control (anyone else experiencing the joys of working with subfertile transgenic animal models?)These samples produce extremely low yields after processing, so that many of them are unusable.Even when I am done processing them, the analysis of this data set is fraught with perils of all kinds...interpretation of the results is, well, tricky.Although there are lots of possible controls, the low yield (see #2) makes it impossible to run all of them so I have to guess as to which potential confounding factor is the most likely and pick the correspondingly appropriate control, and hope that I'm right.Often the most likely confounding factor is contamination. Despite all the necessary precautions during processing, this can still be a problem and while I have good controls (see #4) to determine whether samples are indeed contaminated at the final analysis step, this information renders the sample completely useless and there is no foreseeable way to salvage said sample once the analysis has revealed possible contamination (see #3) and I flatly refuse to try to generate yet another round of replicates for these samples (see #1).Even if all the processing and analysis goes relatively OK, I'm not sure that this data set will be accepted for publication since the analysis will be fraught (see#3), and I can already imagine reviewers suggesting myriad other methodologies for answering the same question, which would be extremely useful were it not for the fact that the yield is so bad (see #2) that running several methodologies on this data set is just impossible.Finally, I have been loathe to finish up with this set because even if everything works beautifully, even if I get sufficient yield, and clear controls, and an obvious result, one possible result from this data set could blow a big hole in the middle of my whole story. Let's hope I get the other possible result, because I would really like to write this up and move on. [I know, I know, I'm a bad scientist -- we should all be unbiased and any result is a good result, blah, blah, blah. Really, people, who do you think you're kidding with that line? There are other ways to salvage this story if I get the undesired result, but it will take a lot longer to finish this project and frankly, I have been working on it for too long already.]There's my whine for the day. If you're looking for me I'll probably be in the lab for the next 12 hours or so.
Labels: Looking Forward