probe sets

[MelD]

Hello,

I am new to the site and have a few basic questions. Forgive me if
they have been ansewered before. I don't use gene chips or look at
the data from them in my day to day work so this is all a bit new to
me.

I am looking at ITGB6. There are two expression charts which have
different probe sets. One is 208083_s_at and the other 208084_at. Is
there a way to find the sequence of these probes on the site or
another site? The data is slightly different for each and I would
like to compare the sequence to determine why it may be different. If
it is not available on the website can you please provide them?

Also, what exactly does "GeneAtlas U133A, gcma" mean? I assume this
is the name of the plate that was run but does the title have any
significance? And what does the y-axis represent? Does it represent
the same thing on every plate?

Thanks for your help,
Melissa

[John]

Hi Melissa,

You can find the individual probe sequences, as well as the probeset
target sequences at Affymetrix.com. You will be asked to create a
username and password and that will give you access to all sequence
information on the NetAffx portion of their website. From BioGPS, you
can follow the links in the Gene Identifiers panel. Follow the Genome
Location or Reporters links on this panel. This will show you how the
probesets map to the genome and may partly explain the differences in
signal you are seeing between the probesets.

"GeneAtlas U133A, gcma" means that this dataset is an atlas of tissue
expression (GeneAtlas) on an Affymetrix U133A array, using the gcrma
algorithm to process the data.

The y-axes on these graphs are represent normalized, background-
subtracted, and summarized (probes to probeset) intensity of each
probeset.

I hope that helps.

John

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[vishuo.s...@gmail.com]

Hello,

For the  probe set,  208083_s_at, 208083_x_at and the other 208084_at, may I know what is the difference?

If I would like to check human gene expression level , which probe set should I use?

[Andrew Su]

Hello,

John's previous answer is pretty good:

"You can find the individual probe sequences, as well as the probeset
target sequences at Affymetrix.com. You will be asked to create a
username and password and that will give you access to all sequence
information on the NetAffx portion of their website. From BioGPS, you
can follow the links in the Gene Identifiers panel. Follow the Genome
Location or Reporters links on this panel. This will show you how the
probesets map to the genome and may partly explain the differences in
signal you are seeing between the probesets."

There unfortunately is no "right" answer on which probe set to use.

Cheers,
-andrew

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[Vishuo.singapore]

Hi Andrew ,
Many thanks