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  • Microarray Signal Intensity values Published data

    Hi,
    I have one question regarding microarrays,I was checking Published data, and they published signal intensity values for Affymetrix Probe Ids
    NCBI's Gene Expression Omnibus (GEO) is a public archive and resource for gene expression data.

    NCBI's Gene Expression Omnibus (GEO) is a public archive and resource for gene expression data.

    I wanted to check the expression of certain genes in that dataset, so I annotated the Affy_Ids to Gene names

    Eg:
    File Affy_Id Sig.Intensity Gene Species Description
    NEB_RA_rep1_annotate.txt: 1428888_at 130.05 tmem33 Mus musculus transmembrane protein 33
    NEB_RA_rep1_annotate.txt: 1436028_at 469.84 tmem33 Mus musculus transmembrane protein 33
    NEB_RA_rep2_annotate.txt: 1428888_at 104.99 tmem33 Mus musculus transmembrane protein 33
    NEB_RA_rep2_annotate.txt: 1436028_at 420.72 tmem33 Mus musculus transmembrane protein 33
    NEB_RA_rep3_annotate.txt: 1428888_at 67.26 tmem33 Mus musculus transmembrane protein 33
    NEB_RA_rep3_annotate.txt: 1436028_at 290 tmem33 Mus musculus transmembrane protein 33


    I see that for each condition, there are two Affy_Ids annotating to the same gene , with different intensity values. Its confusing to judge the intensity value for a gene in particular condition..
    Any suggestions??

  • #2
    Not many genes have more than 1 probeset mapping to them.

    In the cases where there is more than 1 probeset mapping to the gene,
    it could be that there was evidence for alternative splicing when the array was designed, and the different probesets may represent different transcripts.

    Have a look at the Affymetrix web site, at the NetAffx analysis center, and the UCSC browser for more information.

    Comment


    • #3
      Originally posted by mastal View Post
      Not many genes have more than 1 probeset mapping to them.

      In the cases where there is more than 1 probeset mapping to the gene,
      it could be that there was evidence for alternative splicing when the array was designed, and the different probesets may represent different transcripts.

      Have a look at the Affymetrix web site, at the NetAffx analysis center, and the UCSC browser for more information.
      There are other cases of genes where this kind of situation I can see.. But if thats the case of different transcripts.. seems like it wont give easy solution when we want to eye-pick the genes based on signal intensities and judge for the expression??

      Comment


      • #4
        No, it's not easy for those type of cases.

        Where did you get the probe annotations from?

        Comment


        • #5
          Originally posted by mastal View Post
          No, it's not easy for those type of cases.

          Where did you get the probe annotations from?
          I used DAVID gene_Id conversion tool to annotate affy_Id to gene_names

          Comment


          • #6
            Signal Intensity?

            Hello

            Does the signal intensity value (Affy data) is the related with the expression value of genes? Also, I am curious to know if these value is comparable between different probe from 1 dataset and will help to conclude gene1 is expressed higher than gene2 ?

            Thanks in advance.
            Last edited by jeni; 10-27-2014, 08:08 AM.

            Comment

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