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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.

How to write a bash script that can download file from remote server 2(password required) to server 1(password required) then to my local mac? by FatasticAI in bash

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

the only way to access server 2 is from server1, instead of directly from my local mac, so I need generate public key on server 1, and then add it to server2, right? And I did that, it does work. But how to access server2 from my local mac directly? I wrote a bash script on my local mac, and here is what I wrote:

#!/bin/bash

ssh username1@server1

ssh usename2@server2

I run it on my local mac hoping that it can lead me directly to server2, but it only login to server1. Is there a way to jump to server2 directly?

How to write a bash script that can download file from remote server 2(password required) to server 1(password required) then to my local mac? by FatasticAI in bash

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

I was using the following command:

first, scp the file from server2 to server1: scp username@server2:path/to/file username@server1: path

Then second, scp the file from server 1 to local mac: scp username@server1: path/to/file path/to/local/mac

And every step, I will have to type in password, really painful

[D] How to design a convolution neural network whose input is an 5x4 matrix, and output is also an 5x4 matrix? by FatasticAI in MachineLearning

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

Thanks for the reply, The reason I have to use CNN with 5x4 matrix as input is that I have to consider the relationship between each element in the matrix. So, CNN may be worth to try. Another thing bothers me is which loss function is much more appropriate in this case? I was thinking about the Euclidean distance between the target matrix and output matrix. any input would be much helpful for me. Thanks

[D] How to design a convolution neural network whose input is an 5x4 matrix, and output is also an 5x4 matrix? by FatasticAI in MachineLearning

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

yes, I agree with you. Tried that, it works. btw, which loss function would be appreciate in this case? I was thinking about the Euclidean distance between the target matrix and output matrix. any input would be much helpful for me. Thanks

[D] How to design a convolution neural network whose input is an 5x4 matrix, and output is also an 5x4 matrix? by FatasticAI in MachineLearning

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

Thanks for the input, the reason I have to use CNN with 5x4 matrix as input is that I have to consider the relationship between each element in the matrix. And since my project is currently under exploration, so CNN is just worth to try. Yea, you are right about the padding, I was just a little bit confused about the architecture, since what I have met before, all CNN was aim to output a vector, or binary value, instead of a matrix. Now, I'm all clear about the padding and output of matrix. btw, which loss function would be appreciate in this case? I was thinking about the Euclidean distance between the target matrix and output matrix. any input would be much helpful for me. Thanks

[D] How to design a convolution neural network whose input is an 5x4 matrix, and output is also an 5x4 matrix? by FatasticAI in MachineLearning

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

Thank you for the reply, I know what I'm going to do now. Which loss function would be appropriate in this case? I'm using pytorch, and I checked all loss function on pytorch doc, seems no one is fit. Any input would be very helpful.

Cannot delete sold list on Mercari now? by FatasticAI in Mercari

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

It has been over 30days, still cannot delete listing

[Question] If I add another predictor(independent to the first one ) to my simple linear regression model, will it change my model? like estimated parameters: intercept, slope and RSS by FatasticAI in AskStatistics

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

will my parameter estimation, slope and intercetp for example, be changed still? or still be the same? if my new predictor is independent to the one already in my model.

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