Help with R studio

Question

[emmachristison]

Does anyone know what is wrong with this? it has worked in the past. Also, how do I ensure that all of the graph fits on the pdf export? It cuts off.

pheatmap(log2(data + 1), cluster_rows=T, cluster_cols=F, show_rownames = T, cellwidth = 7)
Error in Math.data.frame(data + 1) : 
  non-numeric variable in data frame: c(NA, NA, NA, NA, NA)
In addition: Warning message:
In Ops.factor(left, right) : ‘+’ not meaningful for factors

Thanks Em

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[WouterDeCoster]

Something is wrong with your data variable - it's not what you think it is. Have a look at it using str(data) and head(data).

[emmachristison]

Hello,

It's what I expect it to be and have used before - a list of genes and the coinciding gene expression number - should I format the cell in a certain way?

Thanks!

[WouterDeCoster]

Can you post str(data)? The warning says there are unexpected factors. Make sure the data types of your variables and columns are correct.

[emmachristison]

These are the first few lines:

'data.frame':   5 obs. of  1405 variables:
 $ X                                : Factor w/ 5 levels "AMBRA1","BNIP3",..: 1 2 3 4 5
 $ E3.1.443.fastq.counts.txt        : int  605 649 174 96 43
 $ E3.1.444.fastq.counts.txt        : int  256 309 96 54 42
 $ E3.1.445.fastq.counts.txt        : int  1004 1209 734 149 121
 $ E3.1.447.fastq.counts.txt        : int  324 377 304 75 90
 $ E3.1.448.fastq.counts.txt        : int  115 144 253 99 34
 $ E3.2.449.fastq.counts.txt        : int  522 92 587 191 188
 $ E3.2.450.fastq.counts.txt        : int  428 231 425 90 74
 $ E3.2.452.fastq.counts.txt        : int  1202 1152 475 33 507

[WouterDeCoster]

AGAIN: I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

And look at the column with name X. That's a factor. You cannot do a factor + 1.

[emmachristison]

The cell on the .csv with the X is blank - how do I resolve the issue?

[WouterDeCoster]

According to the output of str() it's not blank. It at least contains 5 levels "AMBRA1","BNIP3". You can drop the column from data.

[Jean-Karim Heriche]

To complement this, check how you're reading the data. The read.table() function and it's variants read a column of numbers as strings and convert them to factors if they see anything that doesn't look like numbers (like NA for example). Also since R 3.1, numbers with too many digits are also read as strings and converted to factors. See type.convert().

[emmachristison]

Hello!

this is how I am currently reading the .csv:

data <- read.csv("Main Mitophagy Genes.csv") #open count file as data variable
data <- read.csv("Main of Mitophagy Genes.csv", header=T, row.names=1, check.names=F) #make it readable

Thanks Emma

[WouterDeCoster]

AGAIN AGAIN

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

If you want help - spend some effort making your question easy to read.

[Jean-Karim Heriche]

Do you mean you're reading it twice ? Or that these are the two different commands that you've tried ?

Answer 1

[Jean-Karim Heriche]

data+1 will try to add 1 to everything, e.g. including the gene names which are not numeric. The solution is to select only the numeric rows/columns before doing numerical operations. It looks like your gene names are in the first column so data[,-1]+1 should work.