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Sara Ribeiro
Feb 4
log/linear detection
I have a similar question. Previously, I used OmicsPlayground version 2 to analyze my proteomics data
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log/linear detection
I have a similar question. Previously, I used OmicsPlayground version 2 to analyze my proteomics data
Feb 4
Philipp Brunnbauer
Jan 28
Abundance File
Heya, I am new to proteomics. Wanted to know some details on the abundance file. We have been
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Abundance File
Heya, I am new to proteomics. Wanted to know some details on the abundance file. We have been
Jan 28
Prisca
,
Ivo Kwee
3
Jan 13
Normalized expression values in Data Table?
Thanks Ivo! This information is just what I was looking for. On Monday, January 13, 2025 at 2:35:30
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Normalized expression values in Data Table?
Thanks Ivo! This information is just what I was looking for. On Monday, January 13, 2025 at 2:35:30
Jan 13
Chris Gonzales
,
Ivo Kwee
2
Jan 13
OmicsPlayground and Phospho-proteomic analysis?
Yes. You could append the phospho site position to your probe as AAAA_123, or add a second column in
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OmicsPlayground and Phospho-proteomic analysis?
Yes. You could append the phospho site position to your probe as AAAA_123, or add a second column in
Jan 13
Ivo Kwee
2
11/7/24
histogram changed
Thanks for reporting this. This is because for efficiency we have downsampled your data for creating
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histogram changed
Thanks for reporting this. This is because for efficiency we have downsampled your data for creating
11/7/24
Ivo Kwee
2
11/7/24
Keeping duplicated genes separate
Hi. True. Currently duplicated genes/features (rows) are merged by averaging the values. For now, as
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Keeping duplicated genes separate
Hi. True. Currently duplicated genes/features (rows) are merged by averaging the values. For now, as
11/7/24
Ivo Kwee
2
11/7/24
how to treat standard-normalized data (aka. relative expression as percentage)
Hi C.Moritz, Looking at your data, you are most probably dealing with "normalized relative
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how to treat standard-normalized data (aka. relative expression as percentage)
Hi C.Moritz, Looking at your data, you are most probably dealing with "normalized relative
11/7/24
Simao P. B. Teixeira
,
Ivo Kwee
2
11/7/24
Percentage of variation in PCA
Thanks. We have not yet such a feature. But it is a good suggestion and probably we will add it in
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Percentage of variation in PCA
Thanks. We have not yet such a feature. But it is a good suggestion and probably we will add it in
11/7/24
Murat Akand
,
Ivo Kwee
2
11/7/24
Gene modules
The heatmap clusters genes by hierarchical clustering. The number of genes per group is dependent on
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Gene modules
The heatmap clusters genes by hierarchical clustering. The number of genes per group is dependent on
11/7/24
Chris Gonzales
,
Ivo Kwee
2
11/7/24
Max median normalization (MaxMedian)
Hi. MaxMedian is a variant of "median normalization", ie all medians per sample are
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Max median normalization (MaxMedian)
Hi. MaxMedian is a variant of "median normalization", ie all medians per sample are
11/7/24
Christophe Deben
,
Mauro Masiero
2
8/20/24
Batch Correction
Dear User, The current version v3.4.4 only allows for batch correction by providing a batch column in
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Batch Correction
Dear User, The current version v3.4.4 only allows for batch correction by providing a batch column in
8/20/24
Shahab Mirshahvaladi
,
Mauro Masiero
3
11/16/23
setting the FC cutoff for differential expression analysis
Thanks Mauro. I saw the conversation in github. sounds good. On Tuesday, April 18, 2023 at 7:45:53 PM
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setting the FC cutoff for differential expression analysis
Thanks Mauro. I saw the conversation in github. sounds good. On Tuesday, April 18, 2023 at 7:45:53 PM
11/16/23
Sara Ribeiro
,
Mauro Masiero
2
8/23/23
V3_Genesets upload
Dear User, There is indeed an issue with genesets. We opened an ticket related to this. To give
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V3_Genesets upload
Dear User, There is indeed an issue with genesets. We opened an ticket related to this. To give
8/23/23
marios mat
,
Mauro Masiero
2
8/4/23
Support for bacterial strains
Dear User, We do not have yet support for bacterial species, but that development is in the roadmap.
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Support for bacterial strains
Dear User, We do not have yet support for bacterial species, but that development is in the roadmap.
8/4/23
franp...@hotmail.com
,
Mauro Masiero
2
7/13/23
Error when loading data
Dear User, Thanks for using OmicsPlayground! Could you kindly give more details about this ocurrence,
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Error when loading data
Dear User, Thanks for using OmicsPlayground! Could you kindly give more details about this ocurrence,
7/13/23
BigOmics Analytics Team
,
Ivo Kwee
2
5/22/23
Question on FDR testing with logFC threshold
Hi Morgane, I think you are referring to the paper "Testing significance relative to a fold-
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Question on FDR testing with logFC threshold
Hi Morgane, I think you are referring to the paper "Testing significance relative to a fold-
5/22/23
Sara Ribeiro
,
Mauro Masiero
4
5/15/23
Data upload issue
Perfect, good to hear that it's working! I believe 2.8.17 was one of the last beta test versions,
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Data upload issue
Perfect, good to hear that it's working! I believe 2.8.17 was one of the last beta test versions,
5/15/23
Andreea C
,
Mauro Masiero
2
5/12/23
Presenting Proteomics Data
Dear User, Thanks for your message, you could also check the text-based documentation here: https://
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Presenting Proteomics Data
Dear User, Thanks for your message, you could also check the text-based documentation here: https://
5/12/23
Ana Contreras
4/17/23
Data upload issue
Hi, I'm trying to upload new data, but I keep getting disconnected. The error message says "
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Data upload issue
Hi, I'm trying to upload new data, but I keep getting disconnected. The error message says "
4/17/23
Shahab Mirshahvaladi
3/21/23
problem in Cluster features in Beta Version
Hi I an not get any images in Cluster features/Gene map (a). There might be a rendering problem in
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problem in Cluster features in Beta Version
Hi I an not get any images in Cluster features/Gene map (a). There might be a rendering problem in
3/21/23
BigOmics Analytics Team
3/21/23
Can analyse the data with setting the organism to Bos taurus?
[Morgane M. email 21.3.2023] Hi, In addition to this first point, I was wondering how I can analyse
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Can analyse the data with setting the organism to Bos taurus?
[Morgane M. email 21.3.2023] Hi, In addition to this first point, I was wondering how I can analyse
3/21/23
BigOmics Analytics Team
3/15/23
Request: keep old heatmap and iTALK in v3
[Shahab email 14.3.3023] The older version had two options for generating heatmaps while the new one
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Request: keep old heatmap and iTALK in v3
[Shahab email 14.3.3023] The older version had two options for generating heatmaps while the new one
3/15/23
Ivo Kwee
3/15/23
New feature request for v3 like Appyter GEO Reverse Search or Set Comparison
[Shahab, email 13.3.2023] the older version had two options for generating heatmaps while the new one
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New feature request for v3 like Appyter GEO Reverse Search or Set Comparison
[Shahab, email 13.3.2023] the older version had two options for generating heatmaps while the new one
3/15/23
BigOmics Analytics Team
3
3/10/23
upload crashes in new version v3beta
resolved. On Friday, 10 March 2023 at 01:00:27 UTC+1 BigOmics Analytics Team wrote: submitted issue
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upload crashes in new version v3beta
resolved. On Friday, 10 March 2023 at 01:00:27 UTC+1 BigOmics Analytics Team wrote: submitted issue
3/10/23
BigOmics Analytics Team
2
3/2/23
celltype identification/deconvolution
Hi Daniel, Celltype estimation/deconvolution is indeed one of the strong functionalities in
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celltype identification/deconvolution
Hi Daniel, Celltype estimation/deconvolution is indeed one of the strong functionalities in
3/2/23
BigOmics Analytics Team
2
3/1/23
How to do best batch correction?
Hi Marian, You're hitting the right questions and answers. It seems your experiments need batch
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How to do best batch correction?
Hi Marian, You're hitting the right questions and answers. It seems your experiments need batch
3/1/23
Mauro Masiero
2
2/24/23
Questions about batch correlation
Thank you for your email! There is no method of choice for batch correction, our approach is to
unread,
Questions about batch correlation
Thank you for your email! There is no method of choice for batch correction, our approach is to
2/24/23
Paul Cantalupo-NV
,
Ivo Kwee
2
2/23/23
Seurat object support
At the moment not directly. You would need to extract the count matrix and metadata (sample
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Seurat object support
At the moment not directly. You would need to extract the count matrix and metadata (sample
2/23/23
Saimul Islam
,
BigOmics Analytics
2
2/22/23
Computation problem
Hey there. Still having problem with this? On Wednesday, December 21, 2022 at 11:54:59 PM UTC+1
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Computation problem
Hey there. Still having problem with this? On Wednesday, December 21, 2022 at 11:54:59 PM UTC+1
2/22/23
Shahab Mirshahvaladi
, …
Staffan Holmqvist
5
1/13/23
isoforms ACs in input file
I am currently working on TMT proteomics analysis. The software does not (to my knowledge!) handle
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isoforms ACs in input file
I am currently working on TMT proteomics analysis. The software does not (to my knowledge!) handle
1/13/23