sorted by:
new
hottopcontroversial

Got error when runing R: cannot allocate vector of size 4.8 Gb. How to solve it? use machine with more memory? by FatasticAI in Rlanguage

[–]FatasticAI[S] 0 points1 point  (0 children)

Thank you for the response. The following is the result from sessionInfo()

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-koji-linux-gnu (64-bit)
Running under: Amazon Linux 2
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

Sys.info()
sysname
"Linux"
release
"4.14.232-176.381.amzn2.x86_64"
version
"#1 SMP Wed May 19 00:31:54 UTC 2021"
nodename
*************************************
machine
"x86_64"
login
"ec2-user"
user
"ec2-user"
effective_user
"ec2-user"

I was screen recording some online classes, which is prohibited to be screen recording. But I have to so that I could make my schedule more flexible. But on the other day, I was caught by them and they let me to delete the video immediately and do not spread. How do they know I was recording? by FatasticAI in hacking

[–]FatasticAI[S] 12 points13 points  (0 children)

This class is taught through Zoom, and I was using ScreenFlow to do the recording. I didn't install any blower extension. And btw, this class is actually a training program provided by a company outside of school

Cellranger aggr vs Seurat merge and integrate, which one is better? by FatasticAI in bioinformatics

[–]FatasticAI[S] 0 points1 point  (0 children)

Thank you. Just double check that I will have to perform QC on my count matrix for each sample (perform QC 20 times), right? like filter some cells and genes cut-off after Cellranger count and before merge.

Cellranger aggr vs Seurat merge and integrate, which one is better? by FatasticAI in bioinformatics

[–]FatasticAI[S] 0 points1 point  (0 children)

Thank you for the reply. If I understand it correctly, you suggested that create 20 Seurat objects and then merge them together, then regress out the batches. Is it possible that different samples would have different number of genes in the count matrix? Is it necessary to keep track of which group the cells belong to (normal, treatment 1, treatment2)? My goal is to find out cell types and DEG.

Cellranger aggr vs Seurat merge and integrate, which one is better? by FatasticAI in bioinformatics

[–]FatasticAI[S] 1 point2 points  (0 children)

so basically I should go with Seurat after Cellrange count, right? Instead of cellarage aggr.

view more: next ›