Question about "AMLmut_923cells.RData"

[Zifeng-L]

Hi, here.
Thanks for your great work on AML. I want to use these methods for my own data, so I downloaded the dem matrix from your GEO database and tried to repeat your analysis. I wonder to know that how can I get "AMLmut_923cells.RData" from GEO? I checked the data but could not found it. Thanks!

[modalaigh]

Hi @Zifeng-L, did you manage to find out which cells are in the "AMLmut_923cells.RData" file? I currently have the same issue that you did. I downloaded the 35 anno.txt files from GEO for the AML patients and saw that there was a column labelled "MutTranscripts". I initially thought that the cells with entries in this column would represent those cells belonging to "AMLmut_923cells.RData" but when I counted all the cells with entries, I ended up with 939 cells which is a bit more than what I was expecting.

[petervangalen]

If you want to use the mutation data, I suggest loading the .anno.txt files. The MutTranscripts and WtTranscripts columns contain the mutation calls and the number of supporting reads (separated by /)

[yi6kim]

I had the same observation, @modalaigh .
When I constructed the dataset myself using the 35 anno.txt files from GEO (as the .RData itself is not given), I ended up with 939 cells not 923 cells.

[Yousuk-Song]

@yi6kim @modalaigh

Hi, I'm working on the same process, and I'm struggling to build AMLmut_923cells.RData too. Could you tell me how did you ended up with 939?

I see this information on a*nnot.txt.gz
MutTranscripts WtTranscripts
normal malignant
normal malignant
normal malignant
malignant normal

and counting cell_ids in which MutTranscripts==malignant can't make results even close to 900s

I really appreciate for your reply

[yi6kim]

@Yousuk-Song Are you sure you added up all 35 annotation files?

When I iterate through the files:

AML.anno.filenames <- list.files("my_directory", full.names = TRUE, pattern = "AML.*\.anno\.txt$")[1:35]
mut_counts <- c()
for (i in 1:35){
mut_counts[i]= sum(table(read.delim(AML.anno.filenames[i], header = T, na.strings = "")$MutTranscripts))
}
print(mut_counts)

15 45 0 0 3 1 3 27 92 0 0 6 0 146 6 0 0 6 1 367 8 2 37 0 3 0 0 1 0 0 0 21 143 6 0

print(sum(mut_counts))

939

[Yousuk-Song]

Thank You so much! I followed your method, chose cells without "MutTranscripts == normal" and got the same results, 939.

I don't understand why are there no explanation or any mentions about the number '923' in the article.