![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F991320%2Fad6e10124c4369b7e51e343769a459de%2FScreen%20Shot%202019-07-29%20at%2010.55.31%20AM.png?generation=1564412205745465&alt=media\")
I have a hard time understanding the usefulness of controls for the challenge. Can someone try reframing this part in a way that is understandable? Perhaps @chimael again
", "messages": [ { "id": "586238", "postDate": "07/28/2019 21:07:21", "content": "I have a hard time understanding the usefulness of controls for the challenge. Can someone try reframing this part in a way that is understandable? Perhaps @chimael again
", "rawMarkdown": "I have a hard time understanding the usefulness of controls for the challenge. Can someone try reframing this part in a way that is understandable? Perhaps @chimael again", "votes": null }, { "id": "586709", "postDate": "07/29/2019 15:09:54", "content": "Ok here is example (forgive for bad doodling)
\n\nImagine we are looking at single cell:
\n\n
Now lets say we are interested in finding out what will happened if we add certain RNA that inhibits some gene which might have some effect on how cell looks.
\n\n![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F991320%2F8d4af78223147bc396e7470efd3fd4de%2FScreen%20Shot%202019-07-29%20at%2010.59.35%20AM.png?generation=1564412394196678&alt=media\")
Hmm... After Addition of RNA nothing changed... its looks the same ... Well I am not sure... Let me try to do some control... I will now design an experiment where instead of RNA I will add Just a water (negative control) .. Water should have no effect on cells and this will give me someway to compare to my actual experiment.
\n\n![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F991320%2Fb7c447ac39816e58d8432bf5c5a14b90%2FScreen%20Shot%202019-07-29%20at%2011.02.12%20AM.png?generation=1564412562826453&alt=media\")
Wow... look its seems like my nuclea (red circle) looks way smaller with RNA than just with water... so it seems like my RNA probably influence the size of nuclea ?
\n\nCan I be sure??? What if its a just variation... or maybe some experimental artifact. . Let me try to include now a positive control.. .maybe add some RNA which I know for sure will influence size of nuclea ...
\n\n![\"\"](\"https://www.googleapis.com/download/storage/v1/b/kaggle-user-content/o/inbox%2F991320%2Fda9a62931e55a672e71d7af899dad786%2FScreen%20Shot%202019-07-29%20at%2011.05.49%20AM.png?generation=1564412818748802&alt=media\")
Aha! Now it seems like we know the answer. Our RNA indeed have some effect on Nuclea... the reason we can make this conclusion its because we have two controls
\n\n1) Negative control were Ijust added water \n2) Positive control which I know for sure influence the nuclear size
\n\nAnd if I compare my experiment to a positive control I can see they both have smaller nuclea. which means now I can for sure conclude my RNA influence the nuclea size.
\n\nIn biology everything is relative.. if you wanna make a conclusion you have to look on both negative and positive control.
", "rawMarkdown": "Ok here is example (forgive for bad doodling)\n\nImagine we are looking at single cell:\n\n\n\n\nNow lets say we are interested in finding out what will happened if we add certain RNA that inhibits some gene which might have some effect on how cell looks. \n\n\n\n\nHmm... After Addition of RNA nothing changed... its looks the same ... Well I am not sure... Let me try to do some control... I will now design an experiment where instead of RNA I will add Just a water (negative control) .. Water should have no effect on cells and this will give me someway to compare to my actual experiment. \n\n\n\nWow... look its seems like my nuclea (red circle) looks way smaller with RNA than just with water... so it seems like my RNA probably influence the size of nuclea ? \n\nCan I be sure??? What if its a just variation... or maybe some experimental artifact. . Let me try to include now a positive control.. .maybe add some RNA which I know for sure will influence size of nuclea ...\n\n\n\n\n\nAha! Now it seems like we know the answer. Our RNA indeed have some effect on Nuclea... the reason we can make this conclusion its because we have two controls \n\n1) Negative control were Ijust added water \n2) Positive control which I know for sure influence the nuclear size \n\nAnd if I compare my experiment to a positive control I can see they both have smaller nuclea. which means now I can for sure conclude my RNA influence the nuclea size.\n\nIn biology everything is relative.. if you wanna make a conclusion you have to look on both negative and positive control.", "votes": null }, { "id": "588446", "postDate": "07/30/2019 15:31:09", "content": "Thanks @drhabib ! and nice to see you here ;)
", "rawMarkdown": "Thanks @drhabib ! and nice to see you here ;)", "votes": null }, { "id": "588516", "postDate": "07/30/2019 17:37:08", "content": "likewise =)
", "rawMarkdown": "likewise =)", "votes": null }, { "id": "589357", "postDate": "07/31/2019 19:47:35", "content": "Thank you @drhabib , based on your description, it seems like we could discard these controls and the idea of control for this competition then since the goal is to classify siRNA images that are already labeled, e.g. we are not interested in the \"effect\" of the siRNA per se. Am I missing something?
", "rawMarkdown": "Thank you @drhabib , based on your description, it seems like we could discard these controls and the idea of control for this competition then since the goal is to classify siRNA images that are already labeled, e.g. we are not interested in the \"effect\" of the siRNA per se. Am I missing something?", "votes": null }, { "id": "589468", "postDate": "07/31/2019 23:40:59", "content": "On the contrary. The description rom @drhabib shows that using controls are critical.\nFor example, suppose in an experiment due to some external factor (e.g., temperature or humidity), the results are are affected in such a way that all images are brighter (or darker). Using control images, one can adjust for such external factors that affect both the control and query images roughly the same way.
", "rawMarkdown": "On the contrary. The description rom @drhabib shows that using controls are critical.\nFor example, suppose in an experiment due to some external factor (e.g., temperature or humidity), the results are are affected in such a way that all images are brighter (or darker). Using control images, one can adjust for such external factors that affect both the control and query images roughly the same way.", "votes": null }, { "id": "589488", "postDate": "08/01/2019 01:10:15", "content": "This is great response! You have said exactly what I wanted =)
", "rawMarkdown": "This is great response! You have said exactly what I wanted =)", "votes": null }, { "id": "591591", "postDate": "08/04/2019 01:10:44", "content": "Thanks @drhabib @rrezaii , could we push the conversation further and go into ideas about how to use this concept in the context of this competition then? I am sure that will be helpful for other people too if you have any idea or hint on this.
\n\nI am not there yet on my side, still trying to get into bronze/silver without this consideration, which according to other threads it should be more than possible at this point.
", "rawMarkdown": "Thanks @drhabib @rrezaii , could we push the conversation further and go into ideas about how to use this concept in the context of this competition then? I am sure that will be helpful for other people too if you have any idea or hint on this. \n\nI am not there yet on my side, still trying to get into bronze/silver without this consideration, which according to other threads it should be more than possible at this point.", "votes": null } ], "comments": [ { "id": 586709, "author_name": "drhabib", "author_url": "", "post_date": "07/29/2019 15:09:54", "content": "Ok here is example (forgive for bad doodling)
\n\nImagine we are looking at single cell:
\n\n
Now lets say we are interested in finding out what will happened if we add certain RNA that inhibits some gene which might have some effect on how cell looks.
\n\n
Hmm... After Addition of RNA nothing changed... its looks the same ... Well I am not sure... Let me try to do some control... I will now design an experiment where instead of RNA I will add Just a water (negative control) .. Water should have no effect on cells and this will give me someway to compare to my actual experiment.
\n\n
Wow... look its seems like my nuclea (red circle) looks way smaller with RNA than just with water... so it seems like my RNA probably influence the size of nuclea ?
\n\nCan I be sure??? What if its a just variation... or maybe some experimental artifact. . Let me try to include now a positive control.. .maybe add some RNA which I know for sure will influence size of nuclea ...
\n\n
Aha! Now it seems like we know the answer. Our RNA indeed have some effect on Nuclea... the reason we can make this conclusion its because we have two controls
\n\n1) Negative control were Ijust added water \n2) Positive control which I know for sure influence the nuclear size
\n\nAnd if I compare my experiment to a positive control I can see they both have smaller nuclea. which means now I can for sure conclude my RNA influence the nuclea size.
\n\nIn biology everything is relative.. if you wanna make a conclusion you have to look on both negative and positive control.
", "votes": null, "replies": [ { "id": 588446, "author_name": "ratthachat", "author_url": "", "post_date": "07/30/2019 15:31:09", "content": "Thanks @drhabib ! and nice to see you here ;)
", "votes": null, "replies": [] }, { "id": 588516, "author_name": "drhabib", "author_url": "", "post_date": "07/30/2019 17:37:08", "content": "likewise =)
", "votes": null, "replies": [] } ] }, { "id": 589357, "author_name": "michelml", "author_url": "", "post_date": "07/31/2019 19:47:35", "content": "Thank you @drhabib , based on your description, it seems like we could discard these controls and the idea of control for this competition then since the goal is to classify siRNA images that are already labeled, e.g. we are not interested in the \"effect\" of the siRNA per se. Am I missing something?
", "votes": null, "replies": [ { "id": 589468, "author_name": "rrezaii", "author_url": "", "post_date": "07/31/2019 23:40:59", "content": "On the contrary. The description rom @drhabib shows that using controls are critical.\nFor example, suppose in an experiment due to some external factor (e.g., temperature or humidity), the results are are affected in such a way that all images are brighter (or darker). Using control images, one can adjust for such external factors that affect both the control and query images roughly the same way.
", "votes": null, "replies": [] }, { "id": 589488, "author_name": "drhabib", "author_url": "", "post_date": "08/01/2019 01:10:15", "content": "This is great response! You have said exactly what I wanted =)
", "votes": null, "replies": [] }, { "id": 591591, "author_name": "michelml", "author_url": "", "post_date": "08/04/2019 01:10:44", "content": "Thanks @drhabib @rrezaii , could we push the conversation further and go into ideas about how to use this concept in the context of this competition then? I am sure that will be helpful for other people too if you have any idea or hint on this.
\n\nI am not there yet on my side, still trying to get into bronze/silver without this consideration, which according to other threads it should be more than possible at this point.
", "votes": null, "replies": [] } ] } ], "raw_markdown_by_id": { "586238": "I have a hard time understanding the usefulness of controls for the challenge. Can someone try reframing this part in a way that is understandable? Perhaps @chimael again", "586709": "Ok here is example (forgive for bad doodling)\n\nImagine we are looking at single cell:\n\n\n\n\nNow lets say we are interested in finding out what will happened if we add certain RNA that inhibits some gene which might have some effect on how cell looks. \n\n\n\n\nHmm... After Addition of RNA nothing changed... its looks the same ... Well I am not sure... Let me try to do some control... I will now design an experiment where instead of RNA I will add Just a water (negative control) .. Water should have no effect on cells and this will give me someway to compare to my actual experiment. \n\n\n\nWow... look its seems like my nuclea (red circle) looks way smaller with RNA than just with water... so it seems like my RNA probably influence the size of nuclea ? \n\nCan I be sure??? What if its a just variation... or maybe some experimental artifact. . Let me try to include now a positive control.. .maybe add some RNA which I know for sure will influence size of nuclea ...\n\n\n\n\n\nAha! Now it seems like we know the answer. Our RNA indeed have some effect on Nuclea... the reason we can make this conclusion its because we have two controls \n\n1) Negative control were Ijust added water \n2) Positive control which I know for sure influence the nuclear size \n\nAnd if I compare my experiment to a positive control I can see they both have smaller nuclea. which means now I can for sure conclude my RNA influence the nuclea size.\n\nIn biology everything is relative.. if you wanna make a conclusion you have to look on both negative and positive control.", "588446": "Thanks @drhabib ! and nice to see you here ;)", "588516": "likewise =)", "589357": "Thank you @drhabib , based on your description, it seems like we could discard these controls and the idea of control for this competition then since the goal is to classify siRNA images that are already labeled, e.g. we are not interested in the \"effect\" of the siRNA per se. Am I missing something?", "589468": "On the contrary. The description rom @drhabib shows that using controls are critical.\nFor example, suppose in an experiment due to some external factor (e.g., temperature or humidity), the results are are affected in such a way that all images are brighter (or darker). Using control images, one can adjust for such external factors that affect both the control and query images roughly the same way.", "589488": "This is great response! You have said exactly what I wanted =)", "591591": "Thanks @drhabib @rrezaii , could we push the conversation further and go into ideas about how to use this concept in the context of this competition then? I am sure that will be helpful for other people too if you have any idea or hint on this. \n\nI am not there yet on my side, still trying to get into bronze/silver without this consideration, which according to other threads it should be more than possible at this point." }, "source": "meta" }