Entering edit mode
Hi all,
As the subject suggests, I'm getting some weird artifacts in ChIP-chip
data I'm looking at (Aiglent 244k human promoter). This is my first
foray into ChIP-chip analysis, so I'm sorry if these are naive
questions.
Instead of painting a picture w/ a 1000 words, I figure it would be
best to drop a few pictures online if someone has some time to look at
them and can offer some suggestion as to what might be happening.
I have 3 replicates experiments for two different Transcription
Factors. In both cases, two of the three replicates look real screwy,
and 1 of them (for both TFs) looks somehow "ok". The plots shown below
are using the r/gProcessedSignals that from Agilent's feature
extraction software, so their error-corrected/bg-subtracted is being
used. I've also removed the control probes.
For TF1:
The "faux" microarray image looks fine. Here's pic of the Log2 ratios
between the red/green channels:
http://cbio.mskcc.org/~lianos/files/bioconductor/bad1.Log2Ratio.png
Here's the funky MA plot for the same replicate expt:
http://cbio.mskcc.org/~lianos/files/bioconductor/bad1.png
Faux microarray image for "better" replicate of same TF:
http://cbio.mskcc.org/~lianos/files/bioconductor/better1.Log2Ratio.png
MA plot for the better replicate of TF1:
http://cbio.mskcc.org/~lianos/files/bioconductor/better1.png
You can see that at low the low-A values of the plot, there is a
pretty significant density of probes that skew the M values quite
high. They are also there in a smaller amount on the rep2 picture,
(but below the M=0 line).
Does anyone have an intuition as to what might be causing this? I
don't have die-swap experiments, so I'm not sure if it's dye bias.
Even so, is there such thing as intensity-specific dye-bias (to
explain it only happening at low values of A (roughly A < 7)?
The effect is even more exacerbated in TF2:
Here's a "weird" replicate:
http://cbio.mskcc.org/~lianos/files/bioconductor/bad2.png
Here's a more reasonable replicate for TF2:
http://cbio.mskcc.org/~lianos/files/bioconductor/better2.png
The faux log2-ratio images for these arrays look much like the other
ones, ie. there are no obvious smudges, etc.
I'm going to check out what probes correspond to those dark spots in
the low-A range, but in the meantime I was wondering if anybody had
any suggestions.
Thanks for any help,
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College of Cornell University
http://cbio.mskcc.org/~lianos