Body: <p><em><strong>This question has been cross-posted on <a href="https://www.biostars.org/p/9561427/" rel="nofollow noreferrer">Biostars</a> but has not received any answers yet, so I'm posting it here. I'll update here if it gets answered there.</strong></em></p>
  <p>I have downloaded a miRNA expression dataset from NCBI GEO <code>(GSE25631)</code> to study differential gene expression and perform other analyses. As mentioned in GEO, this profiling was performed on GPL8179 Illumina Human v2 MicroRNA expression beadchip. Accordingly, I installed the <code>illuminaHumanv2.db</code> package to annotate the Illumina probe IDs. However, when I tried to convert the Illumina probe IDs to their corresponding gene symbols, it returned <code>NA</code> for all the probes. Can anybody identify the issue with this approach? Here's the R script which I used.</p>
  <pre><code>library(GEOquery)
  library(limma)
  library(illuminaHumanv2.db)
  
  Sys.setenv(VROOM_CONNECTION_SIZE = 256000)
  
  data &lt;- getGEO(GEO = &quot;GSE25631&quot;, 
             destdir = &quot;E:\\GSE25631&quot;,
             GSEMatrix = TRUE,
             AnnotGPL = FALSE,
             getGPL = FALSE,
             parseCharacteristics = TRUE)
  
  data &lt;- data$GSE25631_series_matrix.txt.gz
  
  raw_intensity &lt;- exprs(data)
  
  samples &lt;- as.character(pData(data)[,&quot;title&quot;])
  
  raw_intensity_log &lt;- log2(raw_intensity)
  colnames(raw_intensity_log) &lt;- c(rep(&quot;GBM&quot;, 82), rep(&quot;Normal&quot;, 5))
  
  probe_id &lt;- rownames(raw_intensity_log)
  mapping &lt;- data.frame(Gene = unlist(mget(x = probe_id, envir = illuminaHumanv2SYMBOL, ifnotfound = NA)))
  
  
  
  head(mapping, 10)
                 Gene
  ILMN_3166935   NA
  ILMN_3166938   NA 
  ILMN_3166940   NA
  ILMN_3166941   NA 
  ILMN_3166943   NA
  ILMN_3166944   NA
  ILMN_3166945   NA
  ILMN_3166948   NA
  ILMN_3166952   NA
  ILMN_3166953   NA
  </code></pre>
  <p>The <code>GSE25631_RAW.tar</code> file in the supplementary section has all the Probe ID to Gene mappings but I'm curious to know why this approach didn't work.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-04-24T15:55:45.280Z
Comments.Text: Have you confirmed that the probe names are valid using a different tool? Could this be caused by having windows line endings in your file and those are included when querying? Or, since your `E:\\` path suggests you are using Windows, could it be the other way around and something is inserting a `\r` before every trailing `\n`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-04-25T06:04:06.273Z
Comments.Text: I checked the probe-to-gene mappings present in illuminav2SYMBOL. Surprisingly, none of my probe IDs are present, so it returned NAs. The list doesn't seem to contain any mappings for miRNAs. I ended up using the mapping file provided by the manufacturer.
Comments.UserDisplayName: accibio
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-04-25T11:56:31.667Z
Comments.Text: I closed this as non-reproducible since the issue seems to be very specific to your case and your probe names.
Comments.UserDisplayName: terdon
Tags: <r><bioconductor><microarray><illumina><geoquery>
Title: illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion
ThreadText: # illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion
  
  (Asked by: username_0 on 2023-04-24)
  
  ***This question has been cross-posted on [Biostars](https://www.biostars.org/p/9561427/) but has not received any answers yet, so I'm posting it here. I'll update here if it gets answered there.***
  
  I have downloaded a miRNA expression dataset from NCBI GEO `(GSE25631)` to study differential gene expression and perform other analyses. As mentioned in GEO, this profiling was performed on GPL8179 Illumina Human v2 MicroRNA expression beadchip. Accordingly, I installed the `illuminaHumanv2.db` package to annotate the Illumina probe IDs. However, when I tried to convert the Illumina probe IDs to their corresponding gene symbols, it returned `NA` for all the probes. Can anybody identify the issue with this approach? Here's the R script which I used.
  
  ```
  library(GEOquery)
  library(limma)
  library(illuminaHumanv2.db)
  
  Sys.setenv(VROOM_CONNECTION_SIZE = 256000)
  
  data <- getGEO(GEO = "GSE25631", 
             destdir = "E:\\GSE25631",
             GSEMatrix = TRUE,
             AnnotGPL = FALSE,
             getGPL = FALSE,
             parseCharacteristics = TRUE)
  
  data <- data$GSE25631_series_matrix.txt.gz
  
  raw_intensity <- exprs(data)
  
  samples <- as.character(pData(data)[,"title"])
  
  raw_intensity_log <- log2(raw_intensity)
  colnames(raw_intensity_log) <- c(rep("GBM", 82), rep("Normal", 5))
  
  probe_id <- rownames(raw_intensity_log)
  mapping <- data.frame(Gene = unlist(mget(x = probe_id, envir = illuminaHumanv2SYMBOL, ifnotfound = NA)))
  
  head(mapping, 10)
                 Gene
  ILMN_3166935   NA
  ILMN_3166938   NA 
  ILMN_3166940   NA
  ILMN_3166941   NA 
  ILMN_3166943   NA
  ILMN_3166944   NA
  ILMN_3166945   NA
  ILMN_3166948   NA
  ILMN_3166952   NA
  ILMN_3166953   NA
  
  ```
  
  The `GSE25631_RAW.tar` file in the supplementary section has all the Probe ID to Gene mappings but I'm curious to know why this approach didn't work.
  
  **Tags:** r, bioconductor, microarray, illumina, geoquery
  
  > **Comments:**
  > **username_1**: Have you confirmed that the probe names are valid using a different tool? Could this be caused by having windows line endings in your file and those are included when querying? Or, since your `E:\\` path suggests you are using Windows, could it be the other way around and something is inserting a `\r` before every trailing `\n`?  
  > **username_0**: I checked the probe-to-gene mappings present in illuminav2SYMBOL. Surprisingly, none of my probe IDs are present, so it returned NAs. The list doesn't seem to contain any mappings for miRNAs. I ended up using the mapping file provided by the manufacturer.  
  > **username_1**: I closed this as non-reproducible since the issue seems to be very specific to your case and your probe names.  
  
  ---
  
  ## 0 answers
  
  