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I personally believe that community should offer the answer for the question before any other (even relevant) comment. I opening this thread, because one of the most upvoted answers is starting with statement that one should do something else instead of what the question is asking for.

The first statement is not an answer for the question... This is patronising since there is no alternative ("if anything, use FPKMs" sounds like there is something else than FPKMs to use, no?).

I would suggest to keep these comments (that are often very useful) in the END of the answers, not at the beginning. And if we decide to write them, write them with full explanation and a good alternative, not in this declarative style with a link to a blogpost. I really think that this will help keep the community healthy.

So is it just me who feel it that way?

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  • $\begingroup$ If you are not happy with the language feel free to suggest an edit. $\endgroup$ – zx8754 May 19 '17 at 8:11
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    $\begingroup$ Why is this being closed? It's a meta discussion, so being primarily opinion based isn't a problem. It seems like a perfectly useful discussion to have, why close it? $\endgroup$ – terdon May 21 '17 at 17:20
  • $\begingroup$ I kind of felt that it is really just me, therefore I though that it might be good to close the thread. $\endgroup$ – Kamil S Jaron May 21 '17 at 17:46
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I have an edit in the queue to make the "use FPKMs" a bit clearer.

I'm going to interpret your post as being, "I personally believe that the community should offer actual answers before writing opinionated commentary."

Anyway, putting the comment at the beginning there was highly appropriate. OP was essentially saying, "I'm very new and would like to do something that's almost always a bad idea because I've seen it done in a bunch of papers." Since OP is new, burying the warning at the end would likely result in OP wasting time by actually making FPKMs and then hopefully reading, "Oh, but you shouldn't do any of that, do THIS instead."

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    $\begingroup$ It seems that you are convinced that OP wanted to ask, "what is appropriate measure for differential expression and how to calculate it in R?", then you should suggest an edit of the question. But there might be some reasons why you might want to ask question of RPKMs - for instance reproduction of somebody else study or reviewing a strange looking R code... $\endgroup$ – Kamil S Jaron May 19 '17 at 7:33
  • $\begingroup$ I'm not convinced that OP wanted to ask anything, but past experience dictates that that's likely what was intended. $\endgroup$ – Devon Ryan May 19 '17 at 7:38
  • $\begingroup$ Regarding your edit, I’m tempted to reject it since it changes the meaning. The current sentence is correct (I’m using a subordinate clause starting with “which”). But I agree it could perhaps be made clearer; just not by replacing the subordinate “which” by a non-subordinate “that”. $\endgroup$ – Konrad Rudolph May 20 '17 at 18:21
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The general position on the SE sites I am active on is that if the OP is using the wrong tool, then that should be the first thing to mention. So, if a question asks something like "How can I use ClustalW to align two gene sequences?" I think the first thing to mention is that ClustalW is obsolete and a newer tool like ClustalΩ or any of the various other modern aligners should be used instead. Or if someone asks how to use BLAST to call variants from an NGS dataset, rather than attempting to find some sort of weird hack that would make that possible, we should instead point out that there are far, far better tools for this.

So no, if I feel the OP is barking up the wrong tree, pointing that out and providing an alternative seems like the best way of starting an answer. Why waste time explaining the wrong tool instead of helping the OP choose the right one?

If it's just a question of opinion then yes, that should go at the end or not at all. But if it is a case of an XY problem or simple ignorance on the part of the OP, then pointing out the essential error in their reasoning is probably the most useful thing the answer can do.

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  • $\begingroup$ XY seems very relevant. $\endgroup$ – Kamil S Jaron May 19 '17 at 13:26
  • $\begingroup$ Ha! That it does :) $\endgroup$ – terdon May 19 '17 at 13:29
  • $\begingroup$ I just think, that for XY problem, we should make an effort to find together with OP the real question and then change the question. Probably for OP it does not matter, but for others googling it does. Reformulating questions clearly and explicitly will help a lot people finding correctly linked questions and answers quickly. Maybe it is bit related to this post. $\endgroup$ – Kamil S Jaron May 19 '17 at 19:20
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    $\begingroup$ @KamilSJaron of course, if we think it's an XY problem but can't tell what the OP really wants, we should ask in the comments. However, if the objective is obvious but the method wrong, we should give the right approach. For example, if someone asks how to use blastp bit scores to find distant protein homologs, a good answer would explain that blastp is the wrong tool for this and something like PSI-BLAST or HMMER is much better. $\endgroup$ – terdon May 20 '17 at 11:47
  • $\begingroup$ @Kamil, I think that if a newbie is googling the wrong thing, then a question asking that wrong thing answered with a better question has value. $\endgroup$ – winni2k Jun 19 '17 at 18:19
  • $\begingroup$ @wkretzsch the point of mine was, that we should not assume that what OP meant, but rather invest to clarification of question. In fact, I have more and more impression that it is not that hard here. The most of people are able to describe their problem sufficiently to be answered after few questions of someone from the community. $\endgroup$ – Kamil S Jaron Jun 19 '17 at 18:22
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I personally believe that community should offer the answer for the question before any other (even relevant) comment.

I strongly believe the opposite. We should strive to be helpful. And at the risk of sounding patronising again, it’s not helpful to “help” somebody down the wrong path. Instead, we should correct them. This is the case here.

In fact, I’m usually even stricter: in this particular case there was no harm in also providing a literal answer (i.e. the code that implements FPKMs) but usually I would outright refuse to answer a misguided question, and only focus on alternatives.

The first statement is not an answer for the question... This is patronising since there is no alternative

In fact, the answer did give alternatives, and provided links with further information on the subject.

Given all this, I’d respectfully disagree with your claim that the answer was in any way patronising.

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  • $\begingroup$ All right, seems that it is just me... By the way, I looked at your top posts on other SE - they always answer the question and then explained it in detail. $\endgroup$ – Kamil S Jaron May 20 '17 at 18:57

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