<p>All the data associated with this project is here:</p>
<p><a href="https://www.ncbi.nlm.nih.gov/gds/?term=GSE178646" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/gds/?term=GSE178646</a></p>
<p>The actual download page and project description is here
<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646</a></p>
<p>The dataset you seek <strong>GSE178646_raw_counts</strong> is here:</p>
<p><a href="https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178646&amp;format=file" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE178646&amp;format=file</a></p>
<p>The NPC EHMT1_SNV CF7 cells for <strong>GSM5395222_CF7_kallisto_abundance.tsv.gz</strong> is on the same page <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646" rel="nofollow noreferrer">here</a>.</p>
<p>If you now click on the <strong>GEO2 analysis</strong> on this page it will take your <a href="https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE178646" rel="nofollow noreferrer">here</a> where you select your samples and begin the GEO2 analysis.</p>
<hr />
<p>From the comments,</p>
<p>How to do this?</p>
<p>Its easy simply go to <a href="https://www.ncbi.nlm.nih.gov" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov</a></p>
<p>In the check box search for the option <strong>GEO datasets</strong>, in this example I queried <strong>GSM5395222</strong> in the box. This goes to the search results <a href="https://www.ncbi.nlm.nih.gov/gds/?term=GSM5395222" rel="nofollow noreferrer">here</a>, the top hit called &quot;<strong>1</strong>&quot; is document you want <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646" rel="nofollow noreferrer">here</a>. The very top hit (above the <strong>1</strong>) is actual data in question, minus the project information page.</p>
<p>All the information is within this document and simply use a &quot;search text in webpage&quot; using <strong>GSM5395222</strong></p>

CC BY-SA 4.0
2023-08-08T08:09:43.663Z
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?
Sabrina
CC BY-SA 4.0
2023-08-08T10:24:55.440Z
@Sabrina I've modified the post above to include this information below the `--------`
M__
CC BY-SA 4.0
2023-08-08T14:42:31.817Z
Thank you very much for your help
Sabrina
CC BY-SA 4.0
2023-08-07T22:05:46.947Z
2023-08-08T10:38:02.460Z
2023-08-08T10:38:02.460Z
M__
<p>I am new to both coding and GEO so this may be a silly question.</p>
<p>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?</p>
<p>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.</p>
<p>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.</p>
<p>I am using the data set for Series GSE178646 &quot;CRISPR gene editing and inducible pluripotent stem cell neuronal disease modelling for rare disease diagnosis: EMHM1 genetic variant analysis in Kleefstra Syndrome&quot; and am only interested in CF7-12 but the files that I have downloaded are called <code>&quot;GSM5395222_CF7_kallisto_abundance.tsv.gz&quot;</code> where as in the R script in GEO2R the code has used the file <code>&quot;GSE178646_raw_counts_GRCh38.p13_NCBI.tsv.gz&quot;</code> and I am really not sure where I could access this file.</p>

CC BY-SA 4.0
2023-08-08T08:11:22.270Z
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
Sabrina
CC BY-SA 4.0
2023-08-08T10:12:17.883Z
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.
M__
<geo>
How to find the file names referred to in the R script produced by GEO2R in GEO Accession
# How to find the file names referred to in the R script produced by GEO2R in GEO Accession

(Asked by: username_0 on 2023-08-07)

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.

**Tags:** geo
> **Comments:**
> **username_0**: 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  
> **username_1**: 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.  

---

## 1 answers

### Answer by username_1 on 2023-08-07. Score: 2 | Accepted answer

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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646).

If you now click on the **GEO2 analysis** on this page it will take your [here](https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE178646) 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](https://www.ncbi.nlm.nih.gov/gds/?term=GSM5395222), the top hit called "**1**" is document you want [here](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178646). 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**

> **Comments:**
> **username_0**: 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?  
> **username_1**: @Sabrina I've modified the post above to include this information below the `--------`  
> **username_0**: Thank you very much for your help  

---

