Microarray data normalization and annotation - R tutorial

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  • čas přidán 1. 11. 2021
  • #Rstudio #RMA #Annotation
    For Bioinformatics and NGS Analysis services please contact farhan@jgiconsulting.pk
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    Blog: farhanhaqjahangiri.blogspot.c...
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Komentáře • 63

  • @joydipbarua3647
    @joydipbarua3647 Před 2 lety +2

    waiting for next part of microarray data analysis.

  • @cagataysahin6707
    @cagataysahin6707 Před měsícem

    Thank you very much! It was incredibly helpful

  • @friends5936
    @friends5936 Před 2 lety

    Nice

  • @dennismandere1708
    @dennismandere1708 Před 9 měsíci

    This is splendid👍👍

  • @ProfessorSanoar
    @ProfessorSanoar Před 2 měsíci

    Great video

  • @juanjara2221
    @juanjara2221 Před rokem +1

    Very good content, thank you.
    Do you know how I can work with the GSE27813 dataset?, as it has no -.
    .CEL files but only the normalised and non-normalised tables, how can I load the second one to normalise it myself.

  • @gcbicca
    @gcbicca Před rokem

    Do you have a video that explain how to do the quality control of the raw data in order to see the outliers etc.?

  • @grsbiosciences
    @grsbiosciences Před 2 lety

    When I do same for my soft file, I am getting error sir, it seems doesn’t have gene symbols and I’d . GSE162860

  • @gcbicca
    @gcbicca Před rokem

    Thx for the awesome content, could you please send us the bibliography that you used for do this analysis ?

  • @MyGrandsonJeongjo
    @MyGrandsonJeongjo Před rokem

    is read.celfiles function available in r4.2.2? I tried to download the package, but it says it cannot download nor find the function..

  • @wenzhuye5281
    @wenzhuye5281 Před 2 lety +1

    Thanks for such a wonderful and patience video! it really saves me lots of time, thank you again!!!

  • @prankurawasthi229
    @prankurawasthi229 Před 2 lety +1

    How to generate heat map and volcano graf by using r studio in cancer genes

  • @eirinichrysanthou7358
    @eirinichrysanthou7358 Před 2 lety +1

    very useful video and very well explained thank you :) i would like to ask if this method only applied to microarray affymetrix data? if i apply the same to illumina microarray data would that be wrong? thank you!

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety +1

      No. You need to use the soft file of Illumina. Else would be fine

  • @melraz27
    @melraz27 Před rokem +1

    I can't thank you enough for your informative video! I just have a question, I'm using my own cel files (generated by GeneChip miRNA 4.0 Array) ... where can I download the family.softl file?
    Thank you so much in advance!

    • @FarhanHaqj
      @FarhanHaqj  Před rokem

      You may go to GEO NCBI. Search this platform and then open any study related to this platform. You can find the family.soft file at the end of the page along with other file for the same study.

  • @MohammadSaleem-vl8sn
    @MohammadSaleem-vl8sn Před 2 lety

    Please make vedios using ML and artificial intelligence in molecular biology

  • @ifeoluwaemmanuel5093
    @ifeoluwaemmanuel5093 Před rokem

    How can one normalised Agilent data with.txt.gz file format

  • @hafeezuom1422
    @hafeezuom1422 Před 2 lety

    Salam dear Farhan, guide me please in creating Seurat object in R of SCRNA Seq data of ArrayExpress like E-MTAB-7704. Thanking you in anticipation

  • @aryanch43
    @aryanch43 Před 2 lety

    Do you know how to normalize RNA-Seq data using R?

  • @exploresciencewithpritam465

    Your mydata file showing 54675 obs with 7variable.. While mine is 6105616 obs with only 1 variable.. I am using same gsm and . Soft file used in this tutorial

  • @alaasiddig258
    @alaasiddig258 Před 2 lety +1

    Dear Farahan thank you for the informative video. If I am using my own cel files which are generated by clariom S Affymetrix gene chip from where i can get the family.softl file.

  • @hhhh56hh545
    @hhhh56hh545 Před 2 lety +2

    Help
    Hello farhan haq. thank you for your detailed explanation. I have a problem, as you explained I tried to split the slashes but i get this error:
    columns not found: Gene.Symbols
    I have searched lots of forums and websites but I have not found a solution yet.
    I am a newbie so I'll appreciate if you help me.

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety +1

      Check the header of your file. I think Gene.Symbols may be written differently in your file. Maybe there is no "." in the file or may be there is something else written there. It seems there is no problem with the code, thats why you are not finding any solution online.
      Good luck

    • @hhhh56hh545
      @hhhh56hh545 Před 2 lety +1

      @@FarhanHaqj Thank you for your reply, but I have the same data set as the one you are using in this video. I have been doing almost everything you said in the video but still there is the error. what happens if I skip this step?

    • @gcbicca
      @gcbicca Před rokem +1

      @@hhhh56hh545 You have to open the file and delete the data until the columns ID GB_ACC SPOT_ID etc, in order to have only the columns and probe id.

  • @johirislam8174
    @johirislam8174 Před 2 lety

    Can we able to analyse .cel files with DEseq 2 package.And how can I retrieve gene symbol from the ref id or probe id of .cel files in DEseq 2

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety

      Deseq2 is meant for count data and it should not be applied on microarray data

    • @johirislam8174
      @johirislam8174 Před 2 lety

      @@FarhanHaqj oke.suppose I want to see the common DEG between two dataset.One dataset is count data and the other dataset is for microarray data.So can i perform two different package for these two dataset to find out common DEG individually from that??I mean for microarray the limma package and for count or RNAseq data the DEseq2 package?

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety

      @@johirislam8174 yes

    • @johirislam8174
      @johirislam8174 Před 2 lety

      @@FarhanHaqj I am very confused about the microarray data and count data.Can you kindly explain this?

  • @user-rf1nr1em3c
    @user-rf1nr1em3c Před 8 měsíci

    Hello, when i come to the point to use the Csplit function, i get an error :Error in `[.data.table`(indt, , splitCols, with = FALSE) :
    column(s) not found: Gene.Symbol
    What could be the problem??

    • @FarhanHaqj
      @FarhanHaqj  Před 8 měsíci

      Genesymbol colum is not present. Open the file and put this in header

    • @user-rf1nr1em3c
      @user-rf1nr1em3c Před 8 měsíci

      @@FarhanHaqj I have opened the file and the Gene Symbol column is present. I do not know what is the problem

    • @shahidhafathima6153
      @shahidhafathima6153 Před 3 měsíci

      ​@@user-rf1nr1em3c hello..did u get rectified your error.. itoo face the same error

    • @shahidhafathima6153
      @shahidhafathima6153 Před 3 měsíci

      Please provide the code pls

    • @user-rf1nr1em3c
      @user-rf1nr1em3c Před 3 měsíci

      Unfortunately not. I have found another video with another tutorial that worked for me@@shahidhafathima6153

  • @Nadia-db6nb
    @Nadia-db6nb Před 2 lety

    Thanks for the video. I have a data from GEO but the data is in .txt. How can i run normalization for this?

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety

      Is it Affymetrix data ?

    • @Nadia-db6nb
      @Nadia-db6nb Před 2 lety

      @@FarhanHaqj It's agilent microarrays

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety +1

      @@Nadia-db6nb This tutorial is for Affymetrix. Agilent workflow should be different. Please check this www.biostars.org/p/388949/#388960

  • @MohammadSaleem-vl8sn
    @MohammadSaleem-vl8sn Před 2 lety

    How we can use random forest in GWAS studies

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety

      You may check my random forest video

  • @shilpahindocha1544
    @shilpahindocha1544 Před 2 lety

    Hello sir, it shows an error that I have no gene.symbol in my files.

    • @FarhanHaqj
      @FarhanHaqj  Před 2 lety +1

      So change it with any identifier you want to annotate. Like entrez ID etc

  • @user-pw4fg2sx5n
    @user-pw4fg2sx5n Před 6 měsíci

    My data