Answers.Body: <p>Here are two example of calculations of logFC validated in GEO2R analysis which depends if values are already log2 transformed. During GEOQuery analysis there is calculation to transform where expression set is checked for value distribution and log2 transformation is applied-</p>
  <pre><code>ex &lt;- exprs(gset)
  qx &lt;- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
  LogC &lt;- (qx[5] &gt; 100) ||
            (qx[6]-qx[1] &gt; 50 &amp;&amp; qx[2] &gt; 0)
  if (LogC) { ex[which(ex &lt;= 0)] &lt;- NaN
    exprs(gset) &lt;- log2(ex) }
  </code></pre>
  <p><strong>Example 1:</strong></p>
  <p>=&gt; Sample Values are already log2 Transformed</p>
  <pre><code>n(TumorSamples) = 45
  n(ControlSamples) = 46
  
  a = average(TumorSamples) = 9.199053111
  b = average(ControlSamples) = 4.988139348
  
  logFC = |a - b| = 4.210914
  </code></pre>
  <p><strong>Example 2:</strong>
  =&gt; Sample Values are not log2 transformed</p>
  <pre><code>n(TumorSamples) = 2
  n(ControlSamples) = 2
  
  a = average(log2(TumorSample1) + log2(TumorSample2) ... ) = (log2(84) + log2(21.8)) / 2 = 5.419287
  
  b = average(log2(ControlSample1) + log2(ControlSample2) ... ) = (log2(624) + log2(665)) / 2 = 9.331306
  
  logFC = |a - b| = 3.91202
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-03T14:22:55.027Z
Answers.LastActivityDate: 2021-03-03T14:33:23.793Z
Answers.LastEditDate: 2021-03-03T14:33:23.793Z
Answers.UserDisplayName: Vishal Kumar Sahu
Body: <p>Here is <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181532/" rel="nofollow noreferrer">microarray analysis</a> where author uses GSE50632 series on an  Agilent microarray GPL17660 platform with 4 eligible samples which I guess are GSM1224991, GSM1224992, GSM1224993 and GSM1224994 among which two are healthy and two are patient samples.</p>
  <p>However I found the difference in the calculations-</p>
  <p>Through <a href="https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE50632&amp;platform=GPL16294" rel="nofollow noreferrer">GEO2R analysis</a> table it is-</p>
  <pre><code>ID  adj.P.Val   P.Value t   B   logFC   miRNA_ID_LIST   SPOT_ID
  148000  1.86e-02    5.82e-04    3.47    -0.402958   3.91    hsa-miR-3195    
  </code></pre>
  <p>However in the paper the calculated values are far different specially logFC value.</p>
  <p><a href="https://i.sstatic.net/IyapB.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/IyapB.png" alt="Paper Cited Table" /></a></p>
  <p>What could be the reason for this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-15T16:15:27.680Z
Comments.Text: Thanks for answering your own question @VishalKumarSahu, could you please consider "accepting" your answer. It definitely helps with site stats
Comments.UserDisplayName: M__
Tags: <geo>
Title: Difference in Calculation through GEO2R and difference in Article
ThreadText: # Difference in Calculation through GEO2R and difference in Article
  
  (Asked by: username_0 on 2021-03-03)
  
  Here is [microarray analysis](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181532/) where author uses GSE50632 series on an Agilent microarray GPL17660 platform with 4 eligible samples which I guess are GSM1224991, GSM1224992, GSM1224993 and GSM1224994 among which two are healthy and two are patient samples.
  
  However I found the difference in the calculations-
  
  Through [GEO2R analysis](https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE50632&platform=GPL16294) table it is-
  
  ```
  ID  adj.P.Val   P.Value t   B   logFC   miRNA_ID_LIST   SPOT_ID
  148000  1.86e-02    5.82e-04    3.47    -0.402958   3.91    hsa-miR-3195    
  
  ```
  
  However in the paper the calculated values are far different specially logFC value.
  
  [![Paper Cited Table](https://i.sstatic.net/IyapB.png)](https://i.sstatic.net/IyapB.png)
  
  What could be the reason for this?
  
  **Tags:** geo
  
  > **Comments:**
  > **username_1**: Thanks for answering your own question @username_0, could you please consider "accepting" your answer. It definitely helps with site stats  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2021-03-03. Score: 1 | Accepted answer
  
  Here are two example of calculations of logFC validated in GEO2R analysis which depends if values are already log2 transformed. During GEOQuery analysis there is calculation to transform where expression set is checked for value distribution and log2 transformation is applied-
  
  ```
  ex <- exprs(gset)
  qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
  LogC <- (qx[5] > 100) ||
            (qx[6]-qx[1] > 50 && qx[2] > 0)
  if (LogC) { ex[which(ex <= 0)] <- NaN
    exprs(gset) <- log2(ex) }
  
  ```
  
  **Example 1:**
  
  => Sample Values are already log2 Transformed
  
  ```
  n(TumorSamples) = 45
  n(ControlSamples) = 46
  
  a = average(TumorSamples) = 9.199053111
  b = average(ControlSamples) = 4.988139348
  
  logFC = |a - b| = 4.210914
  
  ```
  
  **Example 2:**
  => Sample Values are not log2 transformed
  
  ```
  n(TumorSamples) = 2
  n(ControlSamples) = 2
  
  a = average(log2(TumorSample1) + log2(TumorSample2) ... ) = (log2(84) + log2(21.8)) / 2 = 5.419287
  
  b = average(log2(ControlSample1) + log2(ControlSample2) ... ) = (log2(624) + log2(665)) / 2 = 9.331306
  
  logFC = |a - b| = 3.91202
  
  ```
  
  
  ---
  
  