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Old 03-18-2014, 09:11 AM   #1
priya
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Default 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
http://www.ncbi.nlm.nih.gov/geo/quer...b=GeoDb_blob90
http://www.ncbi.nlm.nih.gov/geo/quer...acc=GSM1045179
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??
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Old 03-18-2014, 09:23 AM   #2
mastal
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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.
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Old 03-18-2014, 09:31 AM   #3
priya
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Quote:
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??
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Old 03-18-2014, 09:35 AM   #4
mastal
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No, it's not easy for those type of cases.

Where did you get the probe annotations from?
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Old 03-18-2014, 11:53 AM   #5
priya
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Quote:
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
http://david.abcc.ncifcrf.gov/conversion.jsp
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Old 10-27-2014, 08:04 AM   #6
jeni
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Default 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 at 08:08 AM.
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