DESeq2 Error Fix: DESeqDataSetFromMatrix ncol(countData) == nrow(colData) is not TRUE
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- čas přidán 29. 06. 2024
- In this video I address following common errors encountered to create DESeqDataSetFromMatrix using counts matrix and colData (i.e. sample metadata).
• Error in DESeqDataSetFromMatrix(countData = countData, colData = colData, : ncol(countData) == nrow(colData) is not TRUE
• all(colnames(counts_data) == rownames(colData)) is not TRUE
I talk about what these errors mean, why we get these errors and demonstrate how to fix these errors. I hope you find this video helpful! Leave your thoughts in the comment section below!
Link to Code:
DESeq2 Error fix: github.com/kpatel427/CZcamsT...
DESeq2 workflow script: github.com/kpatel427/CZcamsT...
Chapters:
0:00 Intro
1:28 Condition 1: nrow(colData) == ncol(counts_data)
3:27 Condition 2: all(rownames(colData) %in% colnames(counts_data))
5:13 Condition 3: all(colnames(counts_data) == rownames(colData))
7:17 Demo: How to check data for all 3 conditions?
9:52 Demo: How to get column names in counts_data to be in same order as row names in colData?
You can show your support and encouragement by buying me a coffee:
www.buymeacoffee.com/bioinfor...
To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: khushbu_p@hotmail.com
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Many thanks for taking the time to guide us in this crystal-clear way. You are one of the best mentors I have ever had.
Thank you so much! Showing us that one line of code is life changing. Hope you are well and I appreciate all the time and effort you put into each video!
I don't know how hard it is to modify already published youtube slides, but at 2:30 I was confused for a moment because colData was on the left and counts_data on the right, despite the tables being the other way. Though, I was able to push through that confusion, so probably not a huge deal.
You're doing some good work here!
You are the best of the best mam...keep it up...
Thanks a lot. You are truly a magician ^^
Could you make a video on how to generate the counts file you used here and in the DESeq workflow video. Many thanks, you explain things so clearly.
I have a video on my channel that explains how count files are generated: czcams.com/video/lG11JjovJHE/video.html
Hi, firstly thank you for your videos. They have helped me a lot! I am just stuck with one step after doing RNA sq analysis for human samples from RAW files. It's probably something very silly, but I am not able to find out how to make the sample_info file. I made an Excel just by typing and trying to put it in R, but the first column is having the default numbering for the rows. Because of that, the columns of my count data are not corresponding to rows of the sample_info files. I have tried removing it using all kinds of tools, but its not getting removed. Could you please help me with this issue? What is the ideal way to get the sample_info files? It would be great if you could help. Thank you!
Also, my experimental design has different samples, one control with three different treatments. So, I am not very sure how to run DESeq exactly.
hi, thank you for your video. I am still a beginner and I have a question. I used three biological replicates for one treatment. So for one set of count_data (for example, gene1 sample 1 = 45 genes), is it the average of the three biological replicates, or does sample 1 represent one biological replicate? thank you in advance.
Thank you for making me understand. but still im getting error the countdata is nt taking empty cell in the excel and reading it as X ! What do i do
Hi
I have a doubt in your data set. That eventhough u have geneids in one column of countsdata how ur global environment shows 8 variables only in the countsdata file
Thank you for the beautifully explained videos. I have a question regarding the counts data file used here. Should the counts used in this file be normalized? Is there a command in Galaxy that can be used to generate this file. I have used FeatureCounts but I don't think that gives normalized counts
DESeq2 requires counts to be un-normalized.
make a video on how to setup snakemake pipeline or next flow pipeline or redun workflow
My colnames and rownames are the exact names and are in exact order and im still getting false error. Could you help me how to resolve
di meri graduation zoology se hai mei switch kr rhi now im doing msc in bioinformatics pass bta do starting mei kis par focus kru ???plzz must needed your help because sare frnds bol rh hai is feilf mei koi gain nahi hai bas loss hi loss hai
Many thanks. Very knowledgeable video. Can you please make video on blast2go for functional annotation (GO and KEGG) of DEGs.Also I want to learn how miRNA, mRNA, lncRNA and circRNA network can be generated from Sequencing data. Can you share your mail id please?Thanks in advance.
can help me to fix this please? Error in DESeqDataSetFromMatrix(countData = mycounts, colData = metadata, :
could not find function "DESeqDataSetFromMatrix". this happens after installing and loading of DESeq2. NB> I was tried to install and load DESeq2 many times but I can`t fix it.
Hi, hope you're doing well.
I'm a phd student in statistics and I wanna classify genes in a reasonable way. My model works well on simulated data and now I'm looking for a real dataset like this:
I look for a tabular dataset, rows indicate person and columns indicate specific measure about genes.
Imagine we have 80 columns among these 80 columns there are four types of genes( from each we have 20) and now I want to classify them.
The thing is, the number of people can be any number, but the number of genes(columns) should be less than 100 and more importantly, from each type of gene we have almost the same number.for example
Gene type 1: 23
Gene type 2: 20
Gene type 3: 17
Gene type 4: 25
Which means that we have 4 types of genes and the number if columns are 65.
Please please help me if you have such real dataset, I really don't know anything about genes and when I'm searching the net, I get confused.
Plzzzzzzzzz, I really nead help.
I'm looking forward to hearing from you.