User: hamza_karakurt

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Posts by hamza_karakurt

<prev • 23 results • page 1 of 3 • next >
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emptyDrops result is full NAs
... Hello, I am trying to use emptyDrops function of dropletUtils package. I used it on my raw counts data but the results is full of NAs. How can I solve this problem or what can be wrong about my data? Thank you in advance. My sessionInfo: R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin ...
scran scater dropletutils scrna-seq written 10 weeks ago by hamza_karakurt30
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Comment: C: Differential Expression Analysis between conditions of single cell RNA-Seq
... Hello again Aaron, Micheal and thank you for answers. Counting counts and create a pseudo-bulk RNA-Seq is an effective method I see and it is suitable to use on specific cell types but I face another question mark. What if we don't have replicates which mean only 1 data for healthy and 1 data for di ...
written 4 months ago by hamza_karakurt30
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Comment: C: Usage of doubletCells() function before or after the batch correction?
... Thank you Aaron, You approach looks really useful and makes sense. I was thinking the same but just wanted to be sure. After computing doublet scores for each data, I will merge the scores to create a vector (same length as cell number) and assign them into the corrected SingleCellExperiment object ...
written 4 months ago by hamza_karakurt30
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Usage of doubletCells() function before or after the batch correction?
... Hello, I am doing a scRNA-Seq analysis and I want to use doubletCells() function to identify possible doublets. My data comes from 4 different batches and I use fastMNN for batch correction. Which way would be better in this situation? Using doubletCells() for each data before batch correction and ...
scran scater scrna-seq doubletcells written 4 months ago by hamza_karakurt30 • updated 4 months ago by Aaron Lun24k
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Comment: C: Using SC3 with batch corrected MNN values
... Thank you for answer. Actually I am planning to use MNN correction. It is more suitable in my situation and further analyses I am planning. MNN can create a corrected expression matrix but it also have negative values (due to cosine normalization I believe). I took the risk and used SC3 on this corr ...
written 4 months ago by hamza_karakurt30
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Comment: C: Using SC3 with batch corrected MNN values
... Thank you for answer. As you said, negative values effects results as expected. To try it, I used sc3_estimate_k function on both data set itself and reduced dimension (PCA with first 50 PCs in that case), and estimated k was 27 for all data and 5 for reduced dimension. Probably it is not a good way ...
written 4 months ago by hamza_karakurt30
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Using SC3 with batch corrected MNN values
... Hello, I want to use SC3 for data sets from multiple batches. I use fastMNN() function of Scran/Scater package for batch normalization but it does not effect logcounts, it creates a reduced dimension "MNN" that shows the corrected data which also used in clustering step. How can I use SC3 with these ...
scran scater sc3 scrna-seq batch correction written 4 months ago by hamza_karakurt30 • updated 4 months ago by Vladimir Kiselev150
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Dunn Index for Clusters from scRNA-Seq
... Hello everyone, I want to try Dunn Index to validate my clustering results from scRNA-Seq data. I know the Dunn index starts from 0 and goes to infinity and higher results mean better clustering. I tried this method from scRNA-Seq which clustered with buildSNNGraph() function of Scater/Scran package ...
clustering scran scater scrna-seq dunn index written 5 months ago by hamza_karakurt30 • updated 5 months ago by Aaron Lun24k
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Differential Expression Analysis between conditions of single cell RNA-Seq
... Hello everyone, I am working on scRNA-Seq data analysis and I have a technical question. We can combine different scRNA-Seq experiments with batch correction methods such as MNN or CCA. As I know, while doing differential expression analysis we should consider batch effect like Scater/Scran package ...
deseq2 rna-seq scrna-seq differential expression analysis written 5 months ago by hamza_karakurt30 • updated 5 months ago by Michael Love24k
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Comment: C: Modularity values of clusters and Differential Expression in scRNA-Seq
... Thank you Aaron, "Since the MNN correction does not effect the logcounts, we can do DE analysis to different data from different batches without using batch correction. But I am wondering, counts must have a batch effect so we kind of ignore it?" Actually I am using some external methods such as R ...
written 5 months ago by hamza_karakurt30

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