Chromosome View

[schwarze]

Hi!

Here is an absolute beginner question:

I use external SNP data of a dense mouse SNP dataset and include a
selfmade genome information file, which loads successfully.
Unfortunately, the chromosome view is blank - most likely due to this
command line:

Removing SNPs that are homozygous or NoCall across all samples...
2010 SNPs removed

How can I circumvent the deletion of all SNPs? Do I need SNP/Sample
Information files?


All the best, Wibke Schwarzer

[Cheng Li]

Wibke,

Can you try the "LOH analysis" at "Analysis/Chromosome" instead of
"linkage analysis" to not remove SNPs?

Cheng

[schwarze]

Hey Cheng,

I've tried all options (including LOH analysis).

Wibke

[schwarze]

I've thought about it - and maybe it's just not the right program for
the haplotype analysis I want to do.
Each inbred mouse strain is naturally homozygous for each SNP,
although, of course, they do not always share the same allele across
strains. I've tried to add an extra column containing both observed
alleles to get rid of the problem. Still all SNPs get removed.

Do you think, this problem has anything to do with the strain
homozygosity?

[schwarze]

Welcome to DNA-Chip Analyzer (dChip) Version (Sep 23 2005)
Select 'Help/Website' for manual and updates

09/02/09, 09:57

{Group dChip is closed}

{Get external data
Reading data file '\\Rindt\zvi\Wibke\SNP\dense-favorite
+Allele.txt'...
Found 2011 lines
Line 2000
Read data for 2010 SNP markers and 17 arrays

Reading sample information file '\\Rindt\zvi\Wibke\SNP\Sample-inf-
dense-favorite.txt'...
Read 2 sample information columns (besides the first two columns)
for 17 arrays

Treat all the 17 arrays as 17 samples and 17 sample groups

Finished}

[schwarze]

Welcome to dChip (DNA-Chip Analyzer), Build date: May 8 2008
Select 'Help/Website' for manual, user forum and updates.

09/02/09, 11:00

{Get external data
Reading data file '\\Rindt\zvi\Wibke\SNP\dense-favorite
+Allele.txt'...
Found 2011 lines

Found 17 arrays
Line 2000
Read data for 2010 probe sets and 17 arrays; 0 missing values

Reading sample information file 'D:\Sample-inf-dense-

[Cheng Li]

Wibke,

Most likely the SNP calls are not read in. At "Analysis/Get external
data", check "SNP data". After the data reading step, use "Tools/
Export expression value" to confirm the data has been read in
successfully.

Cheng

[schwarze]

Hey Chen,

You are right - the SNP data is not read in. I saved/imported my data
as tab delimited .txt file and checked "SNP data".

SNP ID C57BL/6J AKR/J C3H/HeJ
T61.552948 AA AA AA
T61.552962 CC CC CC
T61.552973 TT TT TT

Any idea, why it's not read in properly?
BTW, thanks alot for your help!!

Wibke

[Cheng Li]

Wibke,

By default dChip expects SNP genotype data to contain AA, AB, BB
calls. Your data contain actual genotypes. Do the following the read
it.

Open your data in Excel, change "SNP ID" to "Mouse", and save the file
in text format. This will signal dChip to convert real genotypes to
AA/BB/AB calls.

Cheng

-----Original Message-----
From: dchip-s...@googlegroups.com
[mailto:dchip-s...@googlegroups.com] On Behalf Of schwarze
Sent: Friday, September 04, 2009 5:17 AM
To: dChip Software

[schwarze]

Hey Cheng,

thanks alot for this hint! The SNPs are read in successfully and I can
observe my genotypes in chromosome view.
Now I'd like to perform a linkage analysis - and I guess it needs to
be nonparametric, since I cannot provide classical pedigree data for
my mouse strains. Is this possible with your program? I've tried to
fake some pedigree data by assigning each individual a distinct
family. Of course I've got an error message: 0 or too many meioses
events (bits) in the pedigree
I thought I could try to use Merlin in this context, but unfortunately
this error message occured: FATAL ERROR - The data set includes no
genetic markers

I'll try CompareLinkage next to solve this problem. I really hope that
I didn't waste your time, as I try to do something with dChip that may
not possible..

Cheers, Wibke