Answers.Body: <p>Specify your genes of interest using the <code>features</code> parameter of the <code>ScaleData()</code> function. If this parameter is not specified, only &quot;variable genes&quot; are scaled and that makes sense, genes that do not demonstrate variability across conditions is not interesting in general. Anyhow, since the  <code>DoHeatmap()</code> would be looking at the &quot;scaled data slot&quot;, it will not be able to find your genes of interest unless they show variation.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-05T17:53:07.080Z
Answers.Text: Thank you. I use sctranscform, I should scale my data before or after sctransform function?
Answers.UserDisplayName: Mahta Mira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-05T17:57:24.787Z
Answers.Text: From their vignette: `Note that this single command replaces NormalizeData(), ScaleData(), and FindVariableFeatures().`
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-05T18:02:25.970Z
Answers.Text: I checked sctransform with or without scale data and the results was different
Answers.UserDisplayName: Mahta Mira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-05T18:28:32.850Z
Answers.Text: 1- Please do not edit your questions extensively, these questions meant to help future users too, now the answer and the question does not match. 2- Please read documentation associated with the functions/packages you use: `SCTransform()` doc says `return.only.var.genes: 
  If set to TRUE the scale.data matrices in output assay are subset to contain only the variable genes; default is TRUE`. 3- Please show some effort, you will learn and develop faster if you learn by doing instead of asking questions on each step.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-05T17:51:07.570Z
Answers.LastActivityDate: 2021-08-05T17:51:07.570Z
Answers.UserDisplayName: haci
Body: <p>I have a Seurat object</p>
  <p>I want to plot a list of genes but I got a warning saying most of genes removed</p>
  <p>I have tried with both <em><strong>my genes of interest</strong></em> and <em><strong>all variable genes</strong></em> but the results is very similar</p>
  <p>Does this mean these genes are basically are not expressed in my data?</p>
  <pre><code>   &gt; t<span class="math-container">$V1
    [1] "IGH"          "IGHV1-2"      "IGHV1-3"      "IGHV1-12"     "IGHV1-8"     
    [6] "IGHV1-14"     "IGHV1-17"     "IGHV1-18"     "IGHV1-24"     "IGHV1-45"    
   [11] "IGHV1-46"     "IGHV1-58"     "IGHV1-67"     "IGHV1-68"     "IGHV1-69"    
   [16] "IGHV1-69D"    "IGHV1-38-4"   "IGHV1-69-2"   "IGHV2-5"      "IGHV2-10"    
   [21] "IGHV2-26"     "IGHV2-70"     "IGHV2-70D"    "IGHV3-6"      "IGHV3-7"     
   [26] "IGHV3-9"      "IGHV3-11"     "IGHV3-13"     "IGHV3-15"     "IGHV3-16"    
   [31] "IGHV3-19"     "IGHV3-20"     "IGHV3-21"     "IGHV3-22"     "IGHV3-23"    
   [36] "IGHV3-25"     "IGHV3-29"     "IGHV3-30"     "IGHV3-30-2"   "IGHV3-30-3"  
   [41] "IGHV3-30-5"   "IGHV3-32"     "IGHV3-33"     "IGHV3-33-2"   "IGHV3-35"    
   [46] "IGHV3-36"     "IGHV3-37"     "IGHV3-38"     "IGHV3-41"     "IGHV3-42"    
   [51] "IGHV3-43"     "IGHV3-43D"    "IGHV3-47"     "IGHV3-48"     "IGHV3-49"    
   [56] "IGHV3-50"     "IGHV3-52"     "IGHV3-53"     "IGHV3-54"     "IGHV3-57"    
   [61] "IGHV3-60"     "IGHV3-62"     "IGHV3-63"     "IGHV3-64"     "IGHV3-65"    
   [66] "IGHV3-66"     "IGHV3-71"     "IGHV3-72"     "IGHV3-73"     "IGHV3-74"    
   [71] "IGHV3-75"     "IGHV3-76"     "IGHV3-79"     "IGHV3-38-3"   "IGHV3-69-1"  
   [76] "IGHV4-4"      "IGHV4-28"     "IGHV4-30-1"   "IGHV4-30-2"   "IGHV4-30-4"  
   [81] "IGHV4-31"     "IGHV4-34"     "IGHV4-39"     "IGHV4-55"     "IGHV4-59"    
   [86] "IGHV4-61"     "IGHV4-80"     "IGHV4-38-2"   "IGHV5-51"     "IGHV5-78"    
   [91] "IGHV5-10-1"   "IGHV6-1"      "IGHV7-4-1"    "IGHV7-40"     "IGHV7-27"    
   [96] "IGHV7-56"     "IGHV7-34-1"   "IGHV7-81"     "IGHVII-1-1"   "IGHVII-15-1" 
  [101] "IGHVII-20-1"  "IGHVII-22-1"  "IGHVII-26-2"  "IGHVII-28-1"  "IGHVII-30-1" 
  [106] "IGHVII-30-21" "IGHVII-31-1"  "IGHVII-33-1"  "IGHVII-40-1"  "IGHVII-43-1" 
  [111] "IGHVII-44-2"  "IGHVII-46-1"  "IGHVII-49-1"  "IGHVII-51-2"  "IGHVII-53-1" 
  [116] "IGHVII-60-1"  "IGHVII-62-1"  "IGHVII-65-1"  "IGHVII-67-1"  "IGHVII-74-1" 
  [121] "IGHVII-78-1"  "IGHVIII-2-1"  "IGHVIII-5-1"  "IGHVIII-5-2"  "IGHVIII-11-1"
  [126] "IGHVIII-13-1" "IGHVIII-16-1" "IGHVIII-22-2" "IGHVIII-25-1" "IGHVIII-26-1"
  [131] "IGHVIII-38-1" "IGHVIII-44"   "IGHVIII-47-1" "IGHV8-51-1"   "IGHVIII-67-2"
  [136] "IGHVIII-67-3" "IGHVIII-67-4" "IGHVIII-76-1" "IGHVIII-82"   "IGHVIV-44-1" 
  [141] "IGHD1-1"      "IGHD1-7"      "IGHD1-14"     "IGHD1-20"     "IGHD1-26"    
  [146] "IGHD2-2"      "IGHD2-8"      "IGHD2-15"     "IGHD2-21"     "IGHD3-3"     
  [151] "IGHD3-9"      "IGHD3-10"     "IGHD3-16"     "IGHD3-22"     "IGHD4-4"     
  [156] "IGHD4-11"     "IGHD4-17"     "IGHD4-23"     "IGHD5-5"      "IGHD5-12"    
  [161] "IGHD5-18"     "IGHD5-24"     "IGHD6-6"      "IGHD6-13"     "IGHD6-19"    
  [166] "IGHD6-25"     "IGHD7-27"     "IGHJ1"        "IGHJ1P"       "IGHJ2"       
  [171] "IGHJ2P"       "IGHJ3"        "IGHJ3P"       "IGHJ4"        "IGHJ5"       
  [176] "IGHJ6"        "IGHA1"        "IGHA2"        "IGHG1"        "IGHG2"       
  [181] "IGHG3"        "IGHG4"        "IGHGP"        "IGHD"         "IGHE"        
  [186] "IGHEP1"       "IGHM"        
  &gt; pbmc=ScaleData(
  +     pbmc,
  +     features = t$</span>V1)
  Centering and scaling data matrix
    |================================================================================| 100%
  &gt; DoHeatmap(pbmc,t<span class="math-container">$V1,group.by = "Condition")
  Warning message:
  In DoHeatmap(pbmc, t$</span>V1, group.by = &quot;Condition&quot;) :
    The following features were omitted as they were not found in the scale.data slot for the SCT assay: IGHEP1, IGHE, IGHJ6, IGHJ5, IGHJ4, IGHJ3P, IGHJ3, IGHJ2P, IGHJ2, IGHJ1P, IGHJ1, IGHD7-27, IGHD6-25, IGHD6-19, IGHD6-13, IGHD6-6, IGHD5-24, IGHD5-18, IGHD5-12, IGHD5-5, IGHD4-23, IGHD4-17, IGHD4-11, IGHD4-4, IGHD3-22, IGHD3-16, IGHD3-10, IGHD3-9, IGHD3-3, IGHD2-21, IGHD2-15, IGHD2-8, IGHD2-2, IGHD1-26, IGHD1-20, IGHD1-14, IGHD1-7, IGHD1-1, IGHVIV-44-1, IGHVIII-82, IGHVIII-76-1, IGHVIII-67-4, IGHVIII-67-3, IGHVIII-67-2, IGHV8-51-1, IGHVIII-47-1, IGHVIII-44, IGHVIII-38-1, IGHVIII-26-1, IGHVIII-25-1, IGHVIII-22-2, IGHVIII-16-1, IGHVIII-13-1, IGHVIII-11-1, IGHVIII-5-2, IGHVIII-5-1, IGHVIII-2-1, IGHVII-78-1, IGHVII-74-1, IGHVII-67-1, IGHVII-65-1, IGHVII-62-1, IGHVII-60-1, IGHVII-53-1, IGHVII-51-2, IGHVII-49-1, IGHVII-46-1, IGHVII-44-2, IGHVII-43-1, IGHVII-40-1, IGHVII-33-1, IGHVII-31-1, IGHVII-30-21, IGHVII-30-1, IGHVII-28-1, IGHVII-26-2, IGHVII-22-1, IGHVII-20-1, IGHVII-15-1, IGHVII-1-1, IGH [... truncated]
  &gt; pbmc=ScaleData(
  +     pbmc,
  +     features =rownames(pbmc))
  Centering and scaling data matrix
    |================================================================================| 100%
  &gt; rm(pbmc)
  &gt; pbmc=readRDS(&quot;pbmc.rds&quot;)
  &gt; pbmc=ScaleData(
  +     pbmc,
  +     features =rownames(pbmc))
  Centering and scaling data matrix
    |================================================================================| 100%
  &gt; DoHeatmap(pbmc,t<span class="math-container">$V1,group.by = "Condition")
  Warning message:
  In DoHeatmap(pbmc, t$</span>V1, group.by = &quot;Condition&quot;) :
    The following features were omitted as they were not found in the scale.data slot for the SCT assay: IGHEP1, IGHE, IGHJ6, IGHJ5, IGHJ4, IGHJ3P, IGHJ3, IGHJ2P, IGHJ2, IGHJ1P, IGHJ1, IGHD7-27, IGHD6-25, IGHD6-19, IGHD6-13, IGHD6-6, IGHD5-24, IGHD5-18, IGHD5-12, IGHD5-5, IGHD4-23, IGHD4-17, IGHD4-11, IGHD4-4, IGHD3-22, IGHD3-16, IGHD3-10, IGHD3-9, IGHD3-3, IGHD2-21, IGHD2-15, IGHD2-8, IGHD2-2, IGHD1-26, IGHD1-20, IGHD1-14, IGHD1-7, IGHD1-1, IGHVIV-44-1, IGHVIII-82, IGHVIII-76-1, IGHVIII-67-4, IGHVIII-67-3, IGHVIII-67-2, IGHV8-51-1, IGHVIII-47-1, IGHVIII-44, IGHVIII-38-1, IGHVIII-26-1, IGHVIII-25-1, IGHVIII-22-2, IGHVIII-16-1, IGHVIII-13-1, IGHVIII-11-1, IGHVIII-5-2, IGHVIII-5-1, IGHVIII-2-1, IGHVII-78-1, IGHVII-74-1, IGHVII-67-1, IGHVII-65-1, IGHVII-62-1, IGHVII-60-1, IGHVII-53-1, IGHVII-51-2, IGHVII-49-1, IGHVII-46-1, IGHVII-44-2, IGHVII-43-1, IGHVII-40-1, IGHVII-33-1, IGHVII-31-1, IGHVII-30-21, IGHVII-30-1, IGHVII-28-1, IGHVII-26-2, IGHVII-22-1, IGHVII-20-1, IGHVII-15-1, IGHVII-1-1, IGH [... truncated]
  &gt;
  </code></pre>
  
Tags: <scrnaseq><seurat><10x-genomics><heatmap>
Title: Avoiding the warning 'The following features were omitted as they were not found in the scale.data slot for the SCT assay' in Seurat
ThreadText: # Avoiding the warning 'The following features were omitted as they were not found in the scale.data slot for the SCT assay' in Seurat
  
  (Asked by: username_0 on 2021-08-05)
  
  I have a Seurat object
  
  I want to plot a list of genes but I got a warning saying most of genes removed
  
  I have tried with both ***my genes of interest*** and ***all variable genes*** but the results is very similar
  
  Does this mean these genes are basically are not expressed in my data?
  
  ```
     > t$V1
    [1] "IGH"          "IGHV1-2"      "IGHV1-3"      "IGHV1-12"     "IGHV1-8"     
    [6] "IGHV1-14"     "IGHV1-17"     "IGHV1-18"     "IGHV1-24"     "IGHV1-45"    
   [11] "IGHV1-46"     "IGHV1-58"     "IGHV1-67"     "IGHV1-68"     "IGHV1-69"    
   [16] "IGHV1-69D"    "IGHV1-38-4"   "IGHV1-69-2"   "IGHV2-5"      "IGHV2-10"    
   [21] "IGHV2-26"     "IGHV2-70"     "IGHV2-70D"    "IGHV3-6"      "IGHV3-7"     
   [26] "IGHV3-9"      "IGHV3-11"     "IGHV3-13"     "IGHV3-15"     "IGHV3-16"    
   [31] "IGHV3-19"     "IGHV3-20"     "IGHV3-21"     "IGHV3-22"     "IGHV3-23"    
   [36] "IGHV3-25"     "IGHV3-29"     "IGHV3-30"     "IGHV3-30-2"   "IGHV3-30-3"  
   [41] "IGHV3-30-5"   "IGHV3-32"     "IGHV3-33"     "IGHV3-33-2"   "IGHV3-35"    
   [46] "IGHV3-36"     "IGHV3-37"     "IGHV3-38"     "IGHV3-41"     "IGHV3-42"    
   [51] "IGHV3-43"     "IGHV3-43D"    "IGHV3-47"     "IGHV3-48"     "IGHV3-49"    
   [56] "IGHV3-50"     "IGHV3-52"     "IGHV3-53"     "IGHV3-54"     "IGHV3-57"    
   [61] "IGHV3-60"     "IGHV3-62"     "IGHV3-63"     "IGHV3-64"     "IGHV3-65"    
   [66] "IGHV3-66"     "IGHV3-71"     "IGHV3-72"     "IGHV3-73"     "IGHV3-74"    
   [71] "IGHV3-75"     "IGHV3-76"     "IGHV3-79"     "IGHV3-38-3"   "IGHV3-69-1"  
   [76] "IGHV4-4"      "IGHV4-28"     "IGHV4-30-1"   "IGHV4-30-2"   "IGHV4-30-4"  
   [81] "IGHV4-31"     "IGHV4-34"     "IGHV4-39"     "IGHV4-55"     "IGHV4-59"    
   [86] "IGHV4-61"     "IGHV4-80"     "IGHV4-38-2"   "IGHV5-51"     "IGHV5-78"    
   [91] "IGHV5-10-1"   "IGHV6-1"      "IGHV7-4-1"    "IGHV7-40"     "IGHV7-27"    
   [96] "IGHV7-56"     "IGHV7-34-1"   "IGHV7-81"     "IGHVII-1-1"   "IGHVII-15-1" 
  [101] "IGHVII-20-1"  "IGHVII-22-1"  "IGHVII-26-2"  "IGHVII-28-1"  "IGHVII-30-1" 
  [106] "IGHVII-30-21" "IGHVII-31-1"  "IGHVII-33-1"  "IGHVII-40-1"  "IGHVII-43-1" 
  [111] "IGHVII-44-2"  "IGHVII-46-1"  "IGHVII-49-1"  "IGHVII-51-2"  "IGHVII-53-1" 
  [116] "IGHVII-60-1"  "IGHVII-62-1"  "IGHVII-65-1"  "IGHVII-67-1"  "IGHVII-74-1" 
  [121] "IGHVII-78-1"  "IGHVIII-2-1"  "IGHVIII-5-1"  "IGHVIII-5-2"  "IGHVIII-11-1"
  [126] "IGHVIII-13-1" "IGHVIII-16-1" "IGHVIII-22-2" "IGHVIII-25-1" "IGHVIII-26-1"
  [131] "IGHVIII-38-1" "IGHVIII-44"   "IGHVIII-47-1" "IGHV8-51-1"   "IGHVIII-67-2"
  [136] "IGHVIII-67-3" "IGHVIII-67-4" "IGHVIII-76-1" "IGHVIII-82"   "IGHVIV-44-1" 
  [141] "IGHD1-1"      "IGHD1-7"      "IGHD1-14"     "IGHD1-20"     "IGHD1-26"    
  [146] "IGHD2-2"      "IGHD2-8"      "IGHD2-15"     "IGHD2-21"     "IGHD3-3"     
  [151] "IGHD3-9"      "IGHD3-10"     "IGHD3-16"     "IGHD3-22"     "IGHD4-4"     
  [156] "IGHD4-11"     "IGHD4-17"     "IGHD4-23"     "IGHD5-5"      "IGHD5-12"    
  [161] "IGHD5-18"     "IGHD5-24"     "IGHD6-6"      "IGHD6-13"     "IGHD6-19"    
  [166] "IGHD6-25"     "IGHD7-27"     "IGHJ1"        "IGHJ1P"       "IGHJ2"       
  [171] "IGHJ2P"       "IGHJ3"        "IGHJ3P"       "IGHJ4"        "IGHJ5"       
  [176] "IGHJ6"        "IGHA1"        "IGHA2"        "IGHG1"        "IGHG2"       
  [181] "IGHG3"        "IGHG4"        "IGHGP"        "IGHD"         "IGHE"        
  [186] "IGHEP1"       "IGHM"        
  > pbmc=ScaleData(
  +     pbmc,
  +     features = t$V1)
  Centering and scaling data matrix
    |================================================================================| 100%
  > DoHeatmap(pbmc,t$V1,group.by = "Condition")
  Warning message:
  In DoHeatmap(pbmc, t$V1, group.by = "Condition") :
    The following features were omitted as they were not found in the scale.data slot for the SCT assay: IGHEP1, IGHE, IGHJ6, IGHJ5, IGHJ4, IGHJ3P, IGHJ3, IGHJ2P, IGHJ2, IGHJ1P, IGHJ1, IGHD7-27, IGHD6-25, IGHD6-19, IGHD6-13, IGHD6-6, IGHD5-24, IGHD5-18, IGHD5-12, IGHD5-5, IGHD4-23, IGHD4-17, IGHD4-11, IGHD4-4, IGHD3-22, IGHD3-16, IGHD3-10, IGHD3-9, IGHD3-3, IGHD2-21, IGHD2-15, IGHD2-8, IGHD2-2, IGHD1-26, IGHD1-20, IGHD1-14, IGHD1-7, IGHD1-1, IGHVIV-44-1, IGHVIII-82, IGHVIII-76-1, IGHVIII-67-4, IGHVIII-67-3, IGHVIII-67-2, IGHV8-51-1, IGHVIII-47-1, IGHVIII-44, IGHVIII-38-1, IGHVIII-26-1, IGHVIII-25-1, IGHVIII-22-2, IGHVIII-16-1, IGHVIII-13-1, IGHVIII-11-1, IGHVIII-5-2, IGHVIII-5-1, IGHVIII-2-1, IGHVII-78-1, IGHVII-74-1, IGHVII-67-1, IGHVII-65-1, IGHVII-62-1, IGHVII-60-1, IGHVII-53-1, IGHVII-51-2, IGHVII-49-1, IGHVII-46-1, IGHVII-44-2, IGHVII-43-1, IGHVII-40-1, IGHVII-33-1, IGHVII-31-1, IGHVII-30-21, IGHVII-30-1, IGHVII-28-1, IGHVII-26-2, IGHVII-22-1, IGHVII-20-1, IGHVII-15-1, IGHVII-1-1, IGH [... truncated]
  > pbmc=ScaleData(
  +     pbmc,
  +     features =rownames(pbmc))
  Centering and scaling data matrix
    |================================================================================| 100%
  > rm(pbmc)
  > pbmc=readRDS("pbmc.rds")
  > pbmc=ScaleData(
  +     pbmc,
  +     features =rownames(pbmc))
  Centering and scaling data matrix
    |================================================================================| 100%
  > DoHeatmap(pbmc,t$V1,group.by = "Condition")
  Warning message:
  In DoHeatmap(pbmc, t$V1, group.by = "Condition") :
    The following features were omitted as they were not found in the scale.data slot for the SCT assay: IGHEP1, IGHE, IGHJ6, IGHJ5, IGHJ4, IGHJ3P, IGHJ3, IGHJ2P, IGHJ2, IGHJ1P, IGHJ1, IGHD7-27, IGHD6-25, IGHD6-19, IGHD6-13, IGHD6-6, IGHD5-24, IGHD5-18, IGHD5-12, IGHD5-5, IGHD4-23, IGHD4-17, IGHD4-11, IGHD4-4, IGHD3-22, IGHD3-16, IGHD3-10, IGHD3-9, IGHD3-3, IGHD2-21, IGHD2-15, IGHD2-8, IGHD2-2, IGHD1-26, IGHD1-20, IGHD1-14, IGHD1-7, IGHD1-1, IGHVIV-44-1, IGHVIII-82, IGHVIII-76-1, IGHVIII-67-4, IGHVIII-67-3, IGHVIII-67-2, IGHV8-51-1, IGHVIII-47-1, IGHVIII-44, IGHVIII-38-1, IGHVIII-26-1, IGHVIII-25-1, IGHVIII-22-2, IGHVIII-16-1, IGHVIII-13-1, IGHVIII-11-1, IGHVIII-5-2, IGHVIII-5-1, IGHVIII-2-1, IGHVII-78-1, IGHVII-74-1, IGHVII-67-1, IGHVII-65-1, IGHVII-62-1, IGHVII-60-1, IGHVII-53-1, IGHVII-51-2, IGHVII-49-1, IGHVII-46-1, IGHVII-44-2, IGHVII-43-1, IGHVII-40-1, IGHVII-33-1, IGHVII-31-1, IGHVII-30-21, IGHVII-30-1, IGHVII-28-1, IGHVII-26-2, IGHVII-22-1, IGHVII-20-1, IGHVII-15-1, IGHVII-1-1, IGH [... truncated]
  >
  
  ```
  
  **Tags:** scrnaseq, seurat, 10x-genomics, heatmap
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-08-05. Score: 1
  
  Specify your genes of interest using the `features` parameter of the `ScaleData()` function. If this parameter is not specified, only "variable genes" are scaled and that makes sense, genes that do not demonstrate variability across conditions is not interesting in general. Anyhow, since the `DoHeatmap()` would be looking at the "scaled data slot", it will not be able to find your genes of interest unless they show variation.
  
  > **Comments:**
  > **username_0**: Thank you. I use sctranscform, I should scale my data before or after sctransform function?  
  > **username_1**: From their vignette: `Note that this single command replaces NormalizeData(), ScaleData(), and FindVariableFeatures().`  
  > **username_0**: I checked sctransform with or without scale data and the results was different  
  > **username_1**: 1- Please do not edit your questions extensively, these questions meant to help future users too, now the answer and the question does not match. 2- Please read documentation associated with the functions/packages you use: `SCTransform()` doc says `return.only.var.genes:  If set to TRUE the scale.data matrices in output assay are subset to contain only the variable genes; default is TRUE`. 3- Please show some effort, you will learn and develop faster if you learn by doing instead of asking questions on each step.  
  
  ---
  
  