Differential Expression Analysis using DESeq2 in R

Question

[Erina]

Please help me anyone. I have done everything to solve this problem but didn’t get any solution. I am doing differential expression analysis using DESeq2 package of R. Everything is looking okay in my input files. I checked many times, the rownames in sample info file are equal both in name and order with column names in count data file. After uploading the file to R using read.csv, everything is showing equal in environment section. But when I am checking for equalities, it’s showing False. How can I solve this problem? Many packages are not up to date. Can this be a problem?

[ATpoint]

everything is showing equal in environment section. But when I am checking for equalities, it’s showing False

No idea what this means. Please show code to illustrate the problem.

[Erina]

[GenoMax]

You can copy and paste your code and then use 101010 button in the edit window to format it as text to keep it monospaced.

For example your code will look like this after you paste/format it.

library(DESeq2)
library(tidyverse)
library(airway)

[swbarnes2]

Okay, that shows us the problem, but not what we need to solve it.

But, for instance, are you sure that period after the sample name should be there?

[Erina]

[swbarnes2]

Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that?

If you know that colnames(count_data) does not match rownames(colData), can you explain why do you not want to look at what those are?