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?

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

Cheng

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

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

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-
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

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

On Sep 2, 4:38 am, schwarze <schwa...@molgen.mpg.de> wrote:

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!!

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

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..