User: elb

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elb200
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Torino
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Posts by elb

<prev • 108 results • page 1 of 11 • next >
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Comment: C: Combine two independent Seurat analysis into a single one
... For example: SCT assy for analysis1, SCT assay for analysis2, RNA assay for analysis1, RNA assay for analysis2 and so on ...
written 8 days ago by elb200
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Combine two independent Seurat analysis into a single one
... Hi guys, is it possible to combine two independent Seurat objects into a single one? I'm not talking about the merge because the two objects result from two independent analysis meaning that each one has its own @data, @reduction, @pca.component etc. Thank you in advance ...
rna-seq seurat written 8 days ago by elb200 • updated 8 days ago by Ram32k
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Comment: C: Forward and reverse single cell data analysis
... No no it is the practice of the lab but it is not mandatory ...
written 9 days ago by elb200
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Forward and reverse single cell data analysis
... Hi, I have to analyze published scRNA-Seq data. Data are Chromium 10X on NovaSeq6000 and: for each sample I have forward (R1) in lane1 and lane2 (and hence two files) and reverse (R2) in lane1 and lane2 (and hence two files). Totally I have 4 files for sample. I have .fastq files. I usually analyze ...
rna-seq written 9 days ago by elb200 • updated 9 days ago by swbarnes29.6k
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Comment: C: Normalization and batch effects correction in RNA-Seq data
... Dear Kevin, the design of the experiment of the posted question you redirected me to, is al little bit different from my case because I don't have nested design/s. In any case, people suggest, generally, to pre-normalize data in order to remove some high-level variability and then perform batch-corr ...
written 6 months ago by elb200
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Normalization and batch effects correction in RNA-Seq data
... Hi guys, I have a simple question. I have RNA-Seq data from different batches. As suggested looking at many posts on-line I have pre-normalized my data (using the TMM from edgeR) then I have corrected them using Combat and then I have re-normalized them (for the library-size) using DESeq2. My questi ...
combat rna-seq written 6 months ago by elb200 • updated 6 months ago by rpolicastro4.0k
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Comment: C: Survival time computation
... Thank you very much for your help! I also found a column with "year of death".So, based on: age at diagnosis, year of birth and year of death the follow-up can be calculated easily. ...
written 8 months ago by elb200
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Survival time computation
... Hi guys, since I'm a newbie in the field I'm not able to calculate the years of follow-up from the following data: > age days_to_birth days_to_death year_of_birth age_at_diagn days_to_last_follow_up > 71 -26085 1059 1936 26085 330 C ...
survival written 8 months ago by elb200
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Comment: C: Remove cells from Seurat based on a list
... Thank you very much! It works! ...
written 9 months ago by elb200
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Comment: A: Remove cells from Seurat based on a list
... So, basically subsetting on colnames(obj) removes the cells from all slots of the SeuratObject? Meaning @data,@sct @meta.data etc? Thank you very much ...
written 9 months ago by elb200

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