{
  "id": 441072,
  "title": "Is there negative control in the de_train.parquet?",
  "url": "/competitions/open-problems-single-cell-perturbations/discussion/441072",
  "author_name": "",
  "post_date": "2023-09-17T13:30:45.385012200Z",
  "votes": 3,
  "comment_count": 3,
  "views": 0,
  "content": "<p>Hello, guys:</p>\n<p>When I select the elements in the de_train, I choose those whose \"control\" == 1, and it only returns the two positive control data (Dabrafenib &amp; Belinostat), there is no negative control (DMSO). Besides, when I choose the elements by setting the \"sm_name\" == \"DMSO\", it also returns nothing.</p>\n<p>So, is there negative control in the de_train.parquet? If yes, how can I access it?</p>\n<p>Thank you for any response. </p>",
  "messages": [
    {
      "id": "2443026",
      "postDate": "09/17/2023 13:30:45",
      "content": "<p>Hello, guys:</p>\n<p>When I select the elements in the de_train, I choose those whose \"control\" == 1, and it only returns the two positive control data (Dabrafenib &amp; Belinostat), there is no negative control (DMSO). Besides, when I choose the elements by setting the \"sm_name\" == \"DMSO\", it also returns nothing.</p>\n<p>So, is there negative control in the de_train.parquet? If yes, how can I access it?</p>\n<p>Thank you for any response. </p>",
      "rawMarkdown": "Hello, guys:\n\nWhen I select the elements in the de_train, I choose those whose \"control\" == 1, and it only returns the two positive control data (Dabrafenib & Belinostat), there is no negative control (DMSO). Besides, when I choose the elements by setting the \"sm_name\" == \"DMSO\", it also returns nothing.\n\nSo, is there negative control in the de_train.parquet? If yes, how can I access it?\n\nThank you for any response.",
      "votes": null
    },
    {
      "id": "2443426",
      "postDate": "09/17/2023 17:48:29",
      "content": "<p>I am guessing no?</p>\n<p>I haven't digged into the details, but maybe the negative control was used as a proxy for \"before treatment\" / \"no treatment\" to calculate the differential expression. </p>\n<p>Someone more familiar with the protocol please correct me if I am wrong.</p>",
      "rawMarkdown": "I am guessing no?\n\nI haven't digged into the details, but maybe the negative control was used as a proxy for \"before treatment\" / \"no treatment\" to calculate the differential expression. \n\nSomeone more familiar with the protocol please correct me if I am wrong.",
      "votes": null
    },
    {
      "id": "2443669",
      "postDate": "09/17/2023 20:55:57",
      "content": "<p>yeah, I think so too. DMSO might serve as a solvent / transporter for the drugs used in the experiment. So DMSO is used as negative control and not supposed to cause any changes (or if there are small changes then they are equal over all cell treatments and normalised out by taking the ratio). Experiementally it is usually tested upfront if DMSO causes any changes compared to (really) untreated.</p>",
      "rawMarkdown": "yeah, I think so too. DMSO might serve as a solvent / transporter for the drugs used in the experiment. So DMSO is used as negative control and not supposed to cause any changes (or if there are small changes then they are equal over all cell treatments and normalised out by taking the ratio). Experiementally it is usually tested upfront if DMSO causes any changes compared to (really) untreated.",
      "votes": null
    },
    {
      "id": "2444925",
      "postDate": "09/18/2023 14:43:10",
      "content": "<p>Hi! This is a great question. DMSO is used as a solvent (also called vehicle) as <a href=\"https://www.kaggle.com/rahi37\" target=\"_blank\">@rahi37</a> suggests. Experimentally, all compounds we used in this study were dissolved in DMSO, so for the negative control, we add the solvent without any solute (compound) in it.</p>\n<p>This will not be present in the de_train data, because in the differential expression analysis, the compound treatment is represented as a one-hit matrix. The negative control is represented as an all-zeros matrix for the compound variable when performing the differential expression analysis linear regression. Therefore, there is no coefficient associated with this lack-of compound, and no output DE profile.</p>\n<p>Does this make sense? I will update the data page to reflect these compounds.</p>",
      "rawMarkdown": "Hi! This is a great question. DMSO is used as a solvent (also called vehicle) as @rahi37 suggests. Experimentally, all compounds we used in this study were dissolved in DMSO, so for the negative control, we add the solvent without any solute (compound) in it.\n\nThis will not be present in the de_train data, because in the differential expression analysis, the compound treatment is represented as a one-hit matrix. The negative control is represented as an all-zeros matrix for the compound variable when performing the differential expression analysis linear regression. Therefore, there is no coefficient associated with this lack-of compound, and no output DE profile.\n\nDoes this make sense? I will update the data page to reflect these compounds.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2443426,
      "author_name": "qihuaz",
      "author_url": "",
      "post_date": "09/17/2023 17:48:29",
      "content": "<p>I am guessing no?</p>\n<p>I haven't digged into the details, but maybe the negative control was used as a proxy for \"before treatment\" / \"no treatment\" to calculate the differential expression. </p>\n<p>Someone more familiar with the protocol please correct me if I am wrong.</p>",
      "votes": null,
      "replies": [
        {
          "id": 2443669,
          "author_name": "rahi37",
          "author_url": "",
          "post_date": "09/17/2023 20:55:57",
          "content": "<p>yeah, I think so too. DMSO might serve as a solvent / transporter for the drugs used in the experiment. So DMSO is used as negative control and not supposed to cause any changes (or if there are small changes then they are equal over all cell treatments and normalised out by taking the ratio). Experiementally it is usually tested upfront if DMSO causes any changes compared to (really) untreated.</p>",
          "votes": null,
          "replies": []
        }
      ]
    },
    {
      "id": 2444925,
      "author_name": "danielburkhardt",
      "author_url": "",
      "post_date": "09/18/2023 14:43:10",
      "content": "<p>Hi! This is a great question. DMSO is used as a solvent (also called vehicle) as <a href=\"https://www.kaggle.com/rahi37\" target=\"_blank\">@rahi37</a> suggests. Experimentally, all compounds we used in this study were dissolved in DMSO, so for the negative control, we add the solvent without any solute (compound) in it.</p>\n<p>This will not be present in the de_train data, because in the differential expression analysis, the compound treatment is represented as a one-hit matrix. The negative control is represented as an all-zeros matrix for the compound variable when performing the differential expression analysis linear regression. Therefore, there is no coefficient associated with this lack-of compound, and no output DE profile.</p>\n<p>Does this make sense? I will update the data page to reflect these compounds.</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "2443026": "Hello, guys:\n\nWhen I select the elements in the de_train, I choose those whose \"control\" == 1, and it only returns the two positive control data (Dabrafenib & Belinostat), there is no negative control (DMSO). Besides, when I choose the elements by setting the \"sm_name\" == \"DMSO\", it also returns nothing.\n\nSo, is there negative control in the de_train.parquet? If yes, how can I access it?\n\nThank you for any response.",
    "2443426": "I am guessing no?\n\nI haven't digged into the details, but maybe the negative control was used as a proxy for \"before treatment\" / \"no treatment\" to calculate the differential expression. \n\nSomeone more familiar with the protocol please correct me if I am wrong.",
    "2443669": "yeah, I think so too. DMSO might serve as a solvent / transporter for the drugs used in the experiment. So DMSO is used as negative control and not supposed to cause any changes (or if there are small changes then they are equal over all cell treatments and normalised out by taking the ratio). Experiementally it is usually tested upfront if DMSO causes any changes compared to (really) untreated.",
    "2444925": "Hi! This is a great question. DMSO is used as a solvent (also called vehicle) as @rahi37 suggests. Experimentally, all compounds we used in this study were dissolved in DMSO, so for the negative control, we add the solvent without any solute (compound) in it.\n\nThis will not be present in the de_train data, because in the differential expression analysis, the compound treatment is represented as a one-hit matrix. The negative control is represented as an all-zeros matrix for the compound variable when performing the differential expression analysis linear regression. Therefore, there is no coefficient associated with this lack-of compound, and no output DE profile.\n\nDoes this make sense? I will update the data page to reflect these compounds."
  },
  "source": "meta"
}