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I am new to both coding and GEO so this may be a silly question.

I need the raw_counts data set for the GEO data set I am using but data in the downloads box is not the raw_counts. How would I be able to find the raw counts?

As I am new to both I decided to use GEO2R to run an analysis and then to see if I could create the same results using code in R as I new that I could look at the R script for GEO2R if needed.

I was struggling with which of the files I needed to download so I looked at the R script used in GEO2R but the files that are being used are completely different to the ones that I have downloaded.

I am using the data set for Series GSE178646 "CRISPR gene editing and inducible pluripotent stem cell neuronal disease modelling for rare disease diagnosis: EMHM1 genetic variant analysis in Kleefstra Syndrome" and am only interested in CF7-12 but the files that I have downloaded are called "GSM5395222_CF7_kallisto_abundance.tsv.gz" where as in the R script in GEO2R the code has used the file "GSE178646_raw_counts_GRCh38.p13_NCBI.tsv.gz" and I am really not sure where I could access this file.

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    $\begingroup$ Apologies if there appear to be more than one question the only question is how to find the raw counts data in for this dataset. How would you suggest editing the question so it is clear thats the only question $\endgroup$
    – Sabrina
    Aug 8, 2023 at 8:11
  • $\begingroup$ Thanks for the edit @Sabrina, your edit is clearer. The post is fine - it comprised a singular question when I went through it - and was my mistake, apologies. $\endgroup$
    – M__
    Aug 8, 2023 at 10:12

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All the data associated with this project is here:

https://www.ncbi.nlm.nih.gov/gds/?term=GSE178646

The actual download page and project description is here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646

The dataset you seek GSE178646_raw_counts is here:

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178646&format=file

The NPC EHMT1_SNV CF7 cells for GSM5395222_CF7_kallisto_abundance.tsv.gz is on the same page here.

If you now click on the GEO2 analysis on this page it will take your here where you select your samples and begin the GEO2 analysis.


From the comments,

How to do this?

Its easy simply go to https://www.ncbi.nlm.nih.gov

In the check box search for the option GEO datasets, in this example I queried GSM5395222 in the box. This goes to the search results here, the top hit called "1" is document you want here. The very top hit (above the 1) is actual data in question, minus the project information page.

All the information is within this document and simply use a "search text in webpage" using GSM5395222

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    $\begingroup$ Thank you for this, how were you able to find the raw counts data or do I just put raw counts and it will find the data? $\endgroup$
    – Sabrina
    Aug 8, 2023 at 8:09
  • $\begingroup$ @Sabrina I've modified the post above to include this information below the -------- $\endgroup$
    – M__
    Aug 8, 2023 at 10:24
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    $\begingroup$ Thank you very much for your help $\endgroup$
    – Sabrina
    Aug 8, 2023 at 14:42

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