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Search: Posts Made By: lee_sh
Forum: Bioinformatics 05-23-2012, 08:27 AM
Replies: 1
Views: 2,577
Posted By lee_sh
How to convert high version CEL file to low version?

I am processing Affy promoter tiling array data and need to use version 3 (MAS) or 4(GCOS) CEL file for further MAT analysis. However, my CEL data are higher version (AGCC). Anyone has experience to...
Forum: Bioinformatics 10-28-2011, 06:27 PM
Replies: 9
Views: 3,700
Posted By lee_sh
Yes. Strictly, Venn diagram may be not suitable...

Yes. Strictly, Venn diagram may be not suitable for this question if the elements in two sets can not meet the criteria as you discribed. However, the phenomena of one peak overlapping with more is...
Forum: Bioinformatics 10-28-2011, 06:18 PM
Replies: 9
Views: 3,700
Posted By lee_sh
Thanks. The "ambigous" peaks(like one peak in A...

Thanks. The "ambigous" peaks(like one peak in A overlaps two peaks in B) are accepted as one possiblity in my study. Someone suggested me to use gene instead peak for comparison.
Forum: Bioinformatics 10-28-2011, 06:12 PM
Replies: 9
Views: 3,700
Posted By lee_sh
Good answer. Thanks. Maybe I can also use the...

Good answer. Thanks. Maybe I can also use the percentages of each set to draw Venn diagram.
Forum: Bioinformatics 10-28-2011, 09:44 AM
Replies: 9
Views: 3,700
Posted By lee_sh
How to draw Venn digram for two groups peaks

Hi, everyone. I meet a problem in drawing Venn diagram to describe the overlapping of peaks between two groups. I defined one base overlapping between one peak from A and another peak from B as...
Forum: Illumina/Solexa 07-05-2011, 07:51 AM
Replies: 4
Views: 3,015
Posted By lee_sh
Senior Member: In my samples, it is a...

Senior Member: In my samples, it is a peak/enrichment around TSS and a trough around TES. I did twice ChIP-seq: one is not so sharp, but another one is very sharp and affect my decision on the ChIP...
Forum: Illumina/Solexa 07-05-2011, 07:44 AM
Replies: 4
Views: 3,015
Posted By lee_sh
Thank you for your answer and literature. It...

Thank you for your answer and literature. It seems that sonication quality is important for ChIP-seq and the natural enrichment around TSS is hard to avoid.
Forum: Illumina/Solexa 07-04-2011, 09:03 AM
Replies: 4
Views: 3,015
Posted By lee_sh
Why does "Input" sample give a sharp peak around TSS?

Hi. I found this forum by google and this is my first time posting thread here. Now I meet a problem in ChIP-seq. There is a sharp peak around TSS region in my Input samples. Although I have heard...
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