> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/correlation-engine/reference/faq/rna-express-output.md).

# RNA-Express Output Conversion to Bioset

This guide explains how to transform the output of the BaseSpace RNA-Express application into a bioset file suitable for import into Correlation Engine.

![](https://1165879419-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWolK2fDgPCCcGurM8A73%2Fuploads%2Fgit-blob-ef1fea2bb7f288efdf36810696bca6882506bfc8%2F0%20\(2\).png?alt=media)

## Source File

The core content needed is in the `deseq.res.csv` file, found at:

```
RNA-Express-AppResult/differential/<control_vs_comparison>/
```

This file contains 8 comma-separated columns. The columns of interest are:

1. First column (no header) — Entrez gene names
2. `log2FoldChange`
3. `pvalue`
4. `padj`

|         | baseMean | log2FoldChange | lfcSE    | stat     | pvalue   | padj     | status |
| ------- | -------- | -------------- | -------- | -------- | -------- | -------- | ------ |
| DDX11L1 | 0.257395 | 0.093503       | 0.132188 | 0.707353 | 0.479347 | NaN      | Low    |
| WASH7P  | 51.49006 | -0.02556       | 0.273837 | -0.09336 | 0.925619 | 0.953609 | OK     |

## Transformation Steps

### Step 1: Filter Low-Quality Rows

Filter out rows where `status` = `Low` (column 5). This removes rows with `NaN` values that would not be meaningful.

### Step 2: Extract and Rename Columns

Extract columns 1, `log2FoldChange`, `pvalue`, `padj` and rename headers:

| Original                  | New Header  |
| ------------------------- | ----------- |
| (first column, no header) | `Gene name` |
| `pvalue`                  | `p-value`   |
| `padj`                    | `q-value`   |

### Step 3: Choose Fold Change Representation

Decide how to represent differential expression. Options:

| Representation                | Column Header      | Notes                               |
| ----------------------------- | ------------------ | ----------------------------------- |
| log₂ of fold change ratio 0-N | `Log2 fold change` | Keep as-is                          |
| Fold change ratio 0-N         | `Fold change 0-N`  | Convert from log₂                   |
| Directional ±fold change      | `Fold change`      | CE converts log₂ to ±fold on upload |

### Step 4 (Optional): Rename Gene Names to RefSeq Identifiers

CE matches RNA-seq biosets to the correct platform model based on species-specific RefSeq identifiers. Without this step, the bioset is treated as a custom platform.

Mapping files are available for human, mouse, and rat. RNA-seq data from other CE-supported species can be uploaded using gene symbols and will be ingested as custom platforms.

### Step 5: Apply Cutoffs

**Fold change cutoffs:**

| Representation   | Remove rows between       |
| ---------------- | ------------------------- |
| Log₂ fold change | -0.2630344 and +0.2630344 |
| Fold change 0-N  | 0.8333333 and 1.2         |
| ±fold change     | -1.2 and +1.2             |

**Q-value cutoff:** Remove rows with q-value > 0.05.

{% hint style="info" %}
For RNA-seq data, CE uses a q-value cutoff (not p-value). This differs from array studies, where a p-value cutoff of 0.05 is typically applied.
{% endhint %}

### Step 6 (Optional): Add Expression Values

Add median FPKM values for test and control groups:

* Source: `RNA-Express-AppResult/differential/global/genes.counts.csv`
* Calculate FPKM using gene lengths (fragments per kb per million mapped reads)
* Add as `Test expression` and `Control expression` columns (not used in correlations, provided as reference)

### Step 7: Add Header Information

Add a free-text header above the data table:

```
Bioset summary = <study title>
Comparison = <full test group name> vs. <full control group name>
Data pre-processing = FASTQ files were downloaded from Sequence Read Archive (SRA). No other preprocessing was performed.
Analysis summary = Reads aligned to <genome> using STAR; DESeq2 used for differential expression. q-value cutoff 0.05, fold change cutoff ±1.2.
Test expression - Median FPKM expression in <test group name> (total replicates = N)
Control expression - Median FPKM expression in <control group name> (total replicates = N)
Internal ID - <GSE number>_<comparison number>
```

### Step 8: Name and Import

* Rename the file to a descriptive title (≤ 96 characters).
* Import through the CE UI, selecting ranking on **absolute fold change, descending**.

## Final File Format Examples

| Gene name | Log2 fold change | p-value  | q-value  |
| --------- | ---------------- | -------- | -------- |
| WASH7P    | -0.02556         | 0.007739 | 0.012142 |
| LOC729737 | 0.432888         | 0.002186 | 0.003668 |

Or with RefSeq IDs:

| Gene name | Fold change | p-value  | q-value  |
| --------- | ----------- | -------- | -------- |
| 653635    | -1.56044    | 0.007739 | 0.012142 |
| 79854     | 1.575059    | 0.002186 | 0.003668 |


---

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