text: user9449: 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]
  >
  
  
  user3541: 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.
  
original_text: 9449: <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>
   3541: <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>
  