Read Illumina SNP or expression array data

[Cheng Li]

Posted: 23 May 2007 11:09 pm Post subject: Read Illumina SNP or
expression array data

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Alicia,

You may try the "Analysis/Get external data" function. A proper dchip
gene info file should be prepared from Illumina's annotation data.

Cheng

dChip manual link:
http://www.dchip.org/snp.htm#external

--- In dc...@yahoogroups.com, "Alicia Chung" <achung@...> wrote:
Thu May 10, 2007 1:52 pm

Hi Cheng,

Can I use dChip for analysis of Illumina data (human -6 V2) for
expression analysis? How would I go about doing this and what are the
chip related files that I need.

Thanks,

Alicia



Posted: 23 May 2007 11:13 pm Post subject: How I can use dchip to
analyze the Illumina data?

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--- In dc...@yahoogroups.com, swongphayak <no_reply@...> wrote:

Hi All,
This is my frist time to join in dchip group. I aim to used dchip to
analyze my Illumina file, which have the information in file
different
from Affy (example is showed in below). Could you please suggest me
how I can analyze my data?
Thank you,
Sarawut

ChroNo SNP_Position Sample_ID SNP_ID Genotype1 Genotype2 Score
RawIntensity_Red RawIntensity_Green NorIntensity_Red
NorIntensity_Green
Y 2711818 WG0001018-DNAA01_NA18857 rs2058276 G G 0.9762 153 4329
0.028 1.018
Y 2711818 WG0001018-DNAA02_NA19239 rs2058276 G G 0.9762 246 3893
0.044 1.178
Y 2711818 WG0001018-DNAA03_NA18516 rs2058276 G G 0.9762 180 4024
0.025 0.918
Y 2711818 WG0001018-DNAB01_NA19145 rs2058276 G G 0.9762 273 4589
0.027 0.965
Y 2711818 WG0001018-DNAB02_NA19240 rs2058276 - - 0.0000 135 7 0.015
0.002
Y 2711818 WG0001018-DNAB03_NA19172 rs2058276 - - 0.0000 88 0 0.016
0.000
Y 2711818 WG0001018-DNAC01_NA19137 rs2058276 - - 0.0000 92 5 0.025
0.000
Y 2711818 WG0001018-DNAC02_NA18856 rs2058276 G G 0.9762 243 2951
0.029 1.005
Y 2711818 WG0001018-DNAC03_NA19142 rs2058276 G G 0.9762 407 4868
0.040 0.936
Y 2711818 WG0001018-DNAD01_NA19144 rs2058276 G G 0.9762 103 4584
0.020 0.932
Y 2711818 WG0001018-DNAD02_NA18515 rs2058276 G G 0.9762 167 3788
0.012 0.901
Y 2711818 WG0001018-DNAD03_NA18852 rs2058276 - - 0.0000 58 0 0.004
0.001
Y 2711818 WG0001018-DNAE01_NA18855 rs2058276 - - 0.0000 74 0 0.016
0.000
Y 2711818 WG0001018-DNAE02_NA19238 rs2058276 - - 0.0000 123 52 0.012
0.007
Y 2711818 WG0001018-DNAE03_NA19192 rs2058276 G G 0.9762 186 4316
0.034 1.071
Y 2711818 WG0001018-DNAF01_NA19193 rs2058276 - - 0.0000 50 0 0.009
0.000
Y 2711818 WG0001018-DNAF02_NA19139 rs2058276 G G 0.9762 353 7095
0.027 0.922
Y 2711818 WG0001018-DNAF03_NA19160 rs2058276 G G 0.9762 87 3205 0.019
1.015
Y 2711818 WG0001018-DNAG01_NA19143 rs2058276 - - 0.0000 118 0 0.019
0.000
Y 2711818 WG0001018-DNAG02_NA19194 rs2058276 G G 0.9762 120 3708
0.015 0.891
Y 2711818 WG0001018-DNAG03_NA19120 rs2058276 G G 0.9762 49 3448 0.005
0.955


--- In dc...@yahoogroups.com, "Cheng Li" <cli@...> wrote:

Sarawut,

You may use external data format:

http://biosun1.harvard.edu/complab/dchip/snp.htm#external

A dChip-format genome info file will also be needed.

Cheng



Thu Jul 6, 2006 3:46 pm
Hi Wei,

You should convert Illumina SNP information into the following format
(can copy and paste in Excel) and save in text format:

http://biosun1.harvard.edu/complab/dchip/10K_Xba142_genome_info%20hg17.xls

The first 3 columns are required.

Cheng


From: dc...@yahoogroups.com [mailto:dc...@yahoogroups.com] On Behalf
Of wwresearch2006
Sent: Thursday, July 06, 2006 11:22 AM
To: dc...@yahoogroups.com
Subject: [dChip] what kind of genome information file needed for
illumina array?

Hi, Dr. Li:

I tried to do some copy number analysis on illumina array. I have
made the external data file but need genome information file.
I tried mang genome information files on dChip web site but go thte
following message:

Found genome information for fewer than 1/4 probe set; probably
wrong genome information file for this chip type?

Does that mean I need to make my own genome information file? (the
make genome information file function in dchip only do Affy CSV
file.)
All the following information are requred?

Probe Set ID Chromosome Physical Position Genetic Map
Strand dbSNP RS ID

thanks

wei


Posted: 11 Aug 2007 11:58 am Post subject: dChip for illumina
data?

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Dalila,

You are right that dchip truncate means to 1. Mutiplying all values by
10 or 100 should help. Let me know how it goes.

Cheng


From: Dalila Pinto
Sent: Tuesday, April 24, 2007 10:13 AM
Subject: Re: dChip for illumina data?

Hi Chen,

I have been trying to analyse Illumina's data using dChip.
As you suggested, I prepared an external data file using Illumina's
normalized signals. However, I noticed that dChip gives mean values
equal to one when the 'real mean values' are below one [i.e. manually
calculated for each SNP: (Xnormsample1+Ynormsample1)+
(Xnormsample2+Ynormsample2)+ ... / no. samples].
Do you have a suggestion to overcome this? Do you think that this
could be due to the fact that the Illumina normalized values are
'small values' (please see attachment) and would it help to just
multiply these values by 10X or more?

In the attached file, the second and third columns contain the Sum and
Mean values, respectively, for each SNP. The remaining columns were
used as input for dChip.

Dalila


Cheng Li wrote:

You may make a file like this:

http://www.dchip.org/get%20external%20data.htm

The signal column contains X+Y value, and call column contains
genotype calls such as A/B/AB/No Call. The chromosome info can be made
into a dchip genome info file format. The normalization is not an easy
issue and I recommend that you directly use Illumina’s normalized
signals.

Cheng


From: Dalila Pinto
Sent: Monday, January 22, 2007 6:28 PM
Subject: Re: dChip for illumina data?

Hi Cheng,

I attached an example of the output file obtained after using
illumina's self-normalization procedure (enclosed there is also a pdf
file with info on the normalization procedure). The output example
file contains X raw, B raw, A and B allele normalized intensities (X,
Y), and also R and theta, B allele frequency (based on genotyping
data) and Log R ratio (based on the normalized intensities). Do you
have any suggestion on the suitable format required to read into dChip
in order to infer copy number variations (based on the intensities)
and simultaneously be able to read SNP calls?

For info: Illumina suggests that any normalization procedure applied
to Illumina’s genotyping data must be applied on the sub-bead pool
level (note: we are using the Hap650Y infinium array with ~27 sub-bead
pools; a sub-bead pool = a set of beads that were manufactured
together and are located in roughly the same analytical location
(stripe) on a BeadChip).
Infinium products come with predefined cluster files that designate
genotype classes (or clusters) for each SNP. This 'cluster file'
consisting on info from 120 'normal' HapMap samples (CEU). Comparing
sample intensities to this cluster file will usually generate high
genotype calls, can go from 95 to 99%.

Do you think it is advisable to give a try and use instead the
normalization algorithm in dChip for comparison purposes?

Dalila

Cheng Li wrote:

Hi Dalila,

I haven’t tried Illumina array. You may make an external data file
containing SNP calls and SNP signals and read it by “Get external
data”, then try “Analysis/Chromosome”:

http://www.dchip.org/snp.htm#external

Let me know if there is problem or you may send me your example data.

Cheng


From: Dalila Pinto
Sent: Friday, January 19, 2007 5:02 PM
Subject: dChip for illumina data?

Dear Cheng Li,

We have been using your software dChip to analyze Affymetrix array
data and infer copy number variants. We would be very interested to
try dChip also for Illumina data. I was therefore wondering if you
ever tried to use illumina format and if you could provide me some
tool and info regarding this? Many thanks. I also have registered to
the yahoo Dchip group meeting.

Looking forward to hear from you.
Best wishes,

Dalila Pinto