Chip-chip data analysis - oh I wish I were a bioinformatician! (Jun/17/2008 )

hey hey

I am doing histone mod chip-chip and analyse my data with R/Bioconductor/Ringo. I am no bioinformatician! But I have been written a script to analyse my data in R. So I have nice output files of "chip enriched regions". These are in the form Chr12: 1000-2000 (for example). How on earth can I compare results from different experiments to find common areas of enrichment?

Thanks in advance I will have a meeting with the guys who wrote the script soon, but have a bazillion other things to ask them, so don't want to waste their time if this is just a trivial question.

Clare

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Have you done this yet? If not ... could you explain your problem a little more and tell us exactly what those values mean ...

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Hi Perlmunky
Thanks for replying! Ok, so my output is a list of "Chip enriched regions" or chers. Basically, if a genomic region is a cher it will have a significant number of probes bound to it. And so the output is Chr12 - 1000-2000 (for example) for each region. We get at least 1600 different chers for each experiment. And I want to know if it's possible to see if the same cher is present between different experiments. Does that make sense? It is early in the morning!
CLare

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hi clare,
if i'm not mistaken your output should be something like

chr12 - 1000-2000
chr400 - 1600-2000
chr...

and so on, right? and you have different experiments with the same output and want to filter those which appear in all your experiments right? if that is so, it's not too complicated, but i just want to make sure before. regards.

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Yup, that's exactly what I mean Sorry if I wasn't clear enough
Clare

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if you're using a linux based system this is a quick way to compare files:

clare@desktop $ sort file1 file2 | uniq -d

i'm not sure how many files you can compare with it, maybe you could do all of them. if it is complicated by the number of experiment files you've got we'll find something else. good luck.

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Eeep! That looks like double-dutch to me

We are using R/Bioconductor and Activeperl (both Windows based) to analyse and look at our data. So would that command work??
Sorry - I clearly have no idea and am a complete newbie to all this.
I WILL get there though
Clare

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don't panic clare.

there's a command in windows to find differences between two files, it's called fc.exe
you can access it from accesories - system symbol

the detailed information is in this page http://www.ss64.com/nt/fc.html

the inconvenient i find is that it only compares 2 files... does it work for you like that or still not?

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I'll give this fc.exe a go for now. But we'd really like to compare numerous experiments (perhaps up to 60).

Thanks
Clare

Oh, just to confirm - does it find differences??

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oh well...60 is a lot more than i expected... a script to compare them all should do.

yes, it finds differences between the files that's not what you want....

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