Could someone please help me understand the topic? Is the gene expression data measured before or after drug stimulation. The gene expression data I pointed out was in adata_train.parquet.
\nThank you
Could someone please help me understand the topic? Is the gene expression data measured before or after drug stimulation. The gene expression data I pointed out was in adata_train.parquet.
\nThank you
in the Dataset Description it is written after 24 h:
\n\"For this competition, we designed and generated a novel single-cell perturbational dataset in human peripheral blood mononuclear cells (PBMCs). We selected 144 compounds from the Library of Integrated Network-Based Cellular Signatures (LINCS) Connectivity Map dataset (PMID: 29195078) and measured single-cell gene expression profiles after 24 hours of treatment.\"
", "rawMarkdown": "in the Dataset Description it is written after 24 h:\n\n\"For this competition, we designed and generated a novel single-cell perturbational dataset in human peripheral blood mononuclear cells (PBMCs). We selected 144 compounds from the Library of Integrated Network-Based Cellular Signatures (LINCS) Connectivity Map dataset (PMID: 29195078) and measured single-cell gene expression profiles after 24 hours of treatment.\"", "votes": null }, { "id": "2442469", "postDate": "09/17/2023 04:16:06", "content": "Thank you for your reply, so the final differential expression is the value obtained by comparing the stimulation of positive and negative compounds on the same cell, rather than by comparing before and after the stimulation of the drug.I don't know much about these things so I'm a little confused.
", "rawMarkdown": "Thank you for your reply, so the final differential expression is the value obtained by comparing the stimulation of positive and negative compounds on the same cell, rather than by comparing before and after the stimulation of the drug.I don't know much about these things so I'm a little confused.", "votes": null }, { "id": "2443666", "postDate": "09/17/2023 20:50:12", "content": "yeah, this is not written clearly. I'd expect that the fold changes in de_train.parquet are taken to the DMSO control (negative control). Shouldn't be difficult to check….
\nbut @danielburkhardt could you please clarify?
Yes, the comparison is between untreated DMSO negative control wells and treatment wells.
\nI can understand why this is confusing. You're right that one way to measure the cells is to take a sample of cells from the well before treatment and then again after treatment. This would provide paired measurements before and after treatment of the same pool of cells. However, experience shows that there is greater variation between samples of the same well taken across days compared to the variation between samples of independent wells.
\nDoes this make sense? Think of it like a random-controlled trial, where the effect size is measured between different groups of people.
", "rawMarkdown": "Yes, the comparison is between untreated DMSO negative control wells and treatment wells. \n\nI can understand why this is confusing. You're right that one way to measure the cells is to take a sample of cells from the well before treatment and then again after treatment. This would provide paired measurements before and after treatment of the same pool of cells. However, experience shows that there is greater variation between samples of the same well taken across days compared to the variation between samples of independent wells. \n\nDoes this make sense? Think of it like a random-controlled trial, where the effect size is measured between different groups of people.", "votes": null } ], "comments": [ { "id": 2442084, "author_name": "rahi37", "author_url": "", "post_date": "09/16/2023 17:42:13", "content": "in the Dataset Description it is written after 24 h:
\n\"For this competition, we designed and generated a novel single-cell perturbational dataset in human peripheral blood mononuclear cells (PBMCs). We selected 144 compounds from the Library of Integrated Network-Based Cellular Signatures (LINCS) Connectivity Map dataset (PMID: 29195078) and measured single-cell gene expression profiles after 24 hours of treatment.\"
", "votes": null, "replies": [ { "id": 2442469, "author_name": "yanchengwei", "author_url": "", "post_date": "09/17/2023 04:16:06", "content": "Thank you for your reply, so the final differential expression is the value obtained by comparing the stimulation of positive and negative compounds on the same cell, rather than by comparing before and after the stimulation of the drug.I don't know much about these things so I'm a little confused.
", "votes": null, "replies": [ { "id": 2443666, "author_name": "rahi37", "author_url": "", "post_date": "09/17/2023 20:50:12", "content": "yeah, this is not written clearly. I'd expect that the fold changes in de_train.parquet are taken to the DMSO control (negative control). Shouldn't be difficult to check….
\nbut @danielburkhardt could you please clarify?
Yes, the comparison is between untreated DMSO negative control wells and treatment wells.
\nI can understand why this is confusing. You're right that one way to measure the cells is to take a sample of cells from the well before treatment and then again after treatment. This would provide paired measurements before and after treatment of the same pool of cells. However, experience shows that there is greater variation between samples of the same well taken across days compared to the variation between samples of independent wells.
\nDoes this make sense? Think of it like a random-controlled trial, where the effect size is measured between different groups of people.
", "votes": null, "replies": [] } ] } ] } ] } ], "raw_markdown_by_id": { "2441508": "Could someone please help me understand the topic? Is the gene expression data measured before or after drug stimulation. The gene expression data I pointed out was in adata_train.parquet.\nThank you", "2442084": "in the Dataset Description it is written after 24 h:\n\n\"For this competition, we designed and generated a novel single-cell perturbational dataset in human peripheral blood mononuclear cells (PBMCs). We selected 144 compounds from the Library of Integrated Network-Based Cellular Signatures (LINCS) Connectivity Map dataset (PMID: 29195078) and measured single-cell gene expression profiles after 24 hours of treatment.\"", "2442469": "Thank you for your reply, so the final differential expression is the value obtained by comparing the stimulation of positive and negative compounds on the same cell, rather than by comparing before and after the stimulation of the drug.I don't know much about these things so I'm a little confused.", "2443666": "yeah, this is not written clearly. I'd expect that the fold changes in de_train.parquet are taken to the DMSO control (negative control). Shouldn't be difficult to check.... \nbut @danielburkhardt could you please clarify?", "2444949": "Yes, the comparison is between untreated DMSO negative control wells and treatment wells. \n\nI can understand why this is confusing. You're right that one way to measure the cells is to take a sample of cells from the well before treatment and then again after treatment. This would provide paired measurements before and after treatment of the same pool of cells. However, experience shows that there is greater variation between samples of the same well taken across days compared to the variation between samples of independent wells. \n\nDoes this make sense? Think of it like a random-controlled trial, where the effect size is measured between different groups of people." }, "source": "meta" }