Microarray Signal Intensity values Published data

[priya]

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/query/acc.cgi?view=data&acc=GSM1045179&id=12411&db=GeoDb_blob90

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?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??

[mastal]

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.

[priya]

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??

[mastal]

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

Where did you get the probe annotations from?

[priya]

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

[jeni]

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.