snp6.0 call rate is 0

[simon]

Hi, Cheng,
I am  using dChip to analyze the SNP6.0 data.   The output  show
Affymetrix SNP call file 'C:\Command_Console\Data\affysnp6.0-sample1st\E3_5944_CA23_A4_(GenomeWideSNP_6)' not found; you may set call file suffix at 'Open group', such as '.txt'
Set rest genotypes to No Call; can use 'Analysis/Get external data' to read a SNP call file and save to DCP file after 'Open group'
dchip array summary  saying SNP call rate % is 0.
i don't know how can I solve this problem?
Thanks a lot 
Simon

[Cheng Li]

Simon,

 

If you have the genotype call files, set their extension at “Open group/Suffix of txt file”. If not, use Affy software to generate them.

 

Cheng

 

---

[simon]

I exported txt file from affymetrix and save them in the same folder with their CEL file. However, the output still showed like that below. I was wondering it's because affy use birdseed-v2 as suffix and I tried to open group with birdseed-v2 instead of txt. I failed again.

 Could you pls help me on that?

Thanks

Simon

{Open group dChip

Treat this array type as 'SNP 6.0'

Reading in existing binary CDF file C:\Command_Console\Library\GenomeWideSNP_6.cdf.bin (file format 4)...

Search and extract 'CEL' probe data files of chip type 'GenomeWideSNP_6' in 'C:\Command_Console\Data\affy-dchip'...

Found 1: C:\Command_Console\Data\affy-dchip\A12_snp6.0_1st_(GenomeWideSNP_6).CEL

Reading CEL file...

Reading Command Console Generic Data File Format

Column 2650

Affymetrix SNP call file 'C:\Command_Console\Data\affy-dchip\A12_snp6.0_1st_(GenomeWideSNP_6)' not found; you may set call file suffix at 'Open group', such as '.txt'

Set rest genotypes to No Call; can use 'Analysis/Get external data' to read a SNP call file and save to DCP file after 'Open group'

Found 2: C:\Command_Console\Data\affy-dchip\A1_snp6.0_1st_(GenomeWideSNP_6).CEL

Reading CEL file...

Reading Command Console Generic Data File Format

Column 2650

Affymetrix SNP call file 'C:\Command_Console\Data\affy-dchip\A1_snp6.0_1st_(GenomeWideSNP_6)' not found; you may set call file suffix at 'Open group', such as '.txt'

Set rest genotypes to No Call; can use 'Analysis/Get external data' to read a SNP call file and save to DCP file after 'Open group'

Found 3: C:\Command_Console\Data\affy-dchip\A3_snp6.0_1st_(GenomeWideSNP_6).CEL

Reading CEL file...

Reading Command Console Generic Data File Format

Column 2650

Affymetrix SNP call file 'C:\Command_Console\Data\affy-dchip\A3_snp6.0_1st_(GenomeWideSNP_6)' not found; you may set call file suffix at 'Open group', such as '.txt'

Set rest genotypes to No Call; can use 'Analysis/Get external data' to read a SNP call file and save to DCP file after 'Open group'

Found 4: C:\Command_Console\Data\affy-dchip\B10_snp6.0_1st_(GenomeWideSNP_6).CEL

Reading CEL file...

Reading Command Console Generic Data File Format

Column 2650

Affymetrix SNP call file 'C:\Command_Console\Data\affy-dchip\B10_snp6.0_1st_(GenomeWideSNP_6)' not found; you may set call file suffix at 'Open group', such as '.txt'

[Cheng Li]

Can you post the image of your “Open group” dialog? Make sure to set “Open group/Suffix of txt file” as non-empty, e.g. as “.birdseed-v2.txt”.

[simon]

Hi Cheng,

I  have 16 normal tissues and 16 mental disorder tissues and I want to compare their difference of SNP and copy number. When I do normalization , should I regard all samples as one group or I have do normal and disorder group separately .

Thank you very much
Simon

[Cheng Li]

Simon,

 

You should normalize all samples together as one group so that their copy numbers are comparable.

 

dChip support

 

 

---

From: dchip-s...@googlegroups.com [mailto:dchip-s...@googlegroups.com] On Behalf Of simon

Sent: Thursday, May 07, 2009 2:55 PM
To: dchip-s...@googlegroups.com
Subject: [dchip message 241] Re: snp6.0 call rate is 0

[simon]

Hi Cheng,

The question is followed, I finished normalization and  I want to view A/B SNP, the program suddently stop to work showing "not responding". It seems like fail to handle data processing. Could you please help me on that?

Thanks a lot

[simon]

Hi Cheng,

I get an Not enough memory error message when I normalize  53  Affy SNP6.0 chips.

My computer has Windows XP,   E2160 DUAL CPU @1.80GHz,  3.24 GB of  RAM. Please see below.

Thanks a lot

Simon

 

 

Model-based expression

  Obtain expression/signal values using 'Model-based expression' method and '5th percentile of region (PM-only)' as background
    Not enough memory for Theta in Model(): array 29
Expression calculation not completed}

[Cheng Li]

Simon,

 

Can you try to uncheck “Analysis/open group/options/load probe data in memory” and redo modelling?

[simon]

I tried that , still showing erro message.

please see the post below. Should I reduce 500 MB to 200 or less?

Thank you  very much

 

Treat this array type as 'SNP 6.0'

  Reading in existing binary CDF file E:\software\CD_GenomeWideSNP_6_rev3\Full\GenomeWideSNP_6\LibFiles\GenomeWideSNP_6.Full.cdf.bin (file format 4)...

  Obtain expression/signal values using 'Model-based expression' method and '5th percentile of region (PM-only)' as background

  Allocating memory to store probe data...
    Cannot allocate 500 MB memory; you may restart dChip and try again, or reduce 'Tools/Options/Analysis/Memory for MBEI'

[simon]

I reallocate the memory  to 250 MB and succeeded to normalize the chip, however,  when I continue to do chromosome analysis, the error message showed again.  I tried uncheck probe data in memory, it still not work. Should I have to view one chromosome?

Thank you very much

Simon

 

Memory not enough at CHROMOSOME::GetData(). Try restart dChip and uncheck 'Open group/Options/Load probe data in memory', or view only one chromosome
Not completed}

[Cheng Li]

Simon,

 

You can try to view one chromosome at a time, or use the 64 bit dChip on an x64 PC.

 

Cheng

 

[simon]

Hi Cheng,

I am still confused normal matched analysis.Enclosed please find one example from other scientist's publication.  My quesion is how could they show results like that , one paired normal and one tumor sample ,then followed by another pair? As for my study, I have 15 normal controls and 15 patient samples. I  choosed paired normal as reference, but I never can present data like that?

Thanks a lot

Simon

[Cheng Li]

Simon,

 

Use array list file like:

 

N1

T1

---Standardize---

N2

T2

---Standardize---

…

 

Then select “Chromosome/Draw all curves”.

[simon]

Hi Cheng,
How are you. As you suggested, we bought a new workstation 64bit for affymetrix 6.0 data analysis. We have total 40 samples so far and try to start dchip 64bit. However, it still showed out of memory from very beginning.Same error happened  even I tested only 2 samples. To solve the problem,  I tried all ways what I know including uncheck "load probe data in memory", increased "memory for MBEI" to 2000, uncheck "pre-caculate distances" . I don't know what should I do next?
Thanks a lot
Simon

[Cheng Li]

Simon,

 

Try to check “open group/ignore existing dcp file”, “other info/ignore cdf.bin file”.

 

Set "memory for MBEI" to a smaller number (500).

[simon]

Hi Cheng,

your suggestion is greatly helpful.Thanks a lot

I have a quick question about statistic method of copy number variation. What kind of analysis would you recommend for me to compare CNV between normal and patiens?

best

Simon

[simon]

Hi Cheng,

I Exported copy number data and output file is specified as ...xls.  I am wondering  the number showed in EXCLE file is copy number intensity for each case? Could I use those numbe to do statistics analysis?

Thanks

[Cheng Li]

Simon,

 

If you are using “Chromosome/Export SNP data”, the output table contains inferred or raw copy numbers.

Cheng
 

---

From: dchip-s...@googlegroups.com [mailto:dchip-s...@googlegroups.com] On Behalf Of simon
Sent: Thursday, August 27, 2009 2:34 PM
To: dchip-s...@googlegroups.com
Subject: [dchip message 330] Re: snp6.0 call rate is 0

 

Hi Cheng,

I Exported copy number data and output file is specified as ...xls.  I am wondering  the number showed in EXCLE file is copy number intensity for each case? Could I use those numbe to do statistics analysis?

[simon]

Thanks a lot. I have one more question. I viewed copy number with chromosome. However,If I zoom in or out with arrow" up" or "down", the density(the pink color) of same region changed accordingly.I don't know which image indicate their real copy number? 

By the way, I am wondering is there any workshop for dChip in boston recently?

Thanks

Simon

 

 

Hi Cheng,

[Cheng Li]

Simon,

 

Could you attach images of the differences?

 

> What kind of analysis would you recommend for me to compare CNV between normal and patients?

 

One idea could be to export copy numbers according to chromosome regions, then do comparison between the two groups like expression data using t-test or SAM:

http://www.dchip.org/snp_cluster.htm  

 

We don’t have immediate plan for dChip workshop, but will announce it here if we do.

[simon]

Hi Cheng,

I am attaching two copy number pictures of choromosome 1. If I zoom out with the arrow "up", I found top of middle part(1p36.11 region) has higher copy number where showed dense pure pink color. However, If I zoom in , this region didn't show much higher copy number(please see attached zoom in picture). I don't know which image I should trust ?

In addition, I only got the part of intensity values of copy number when I choose "export  data" since the error shows the excel can't show all of them.

thanks  a lot

Simon

[Cheng Li]

Simon,

 

Since each SNP is displayed as a block, in the proportional view it hides many other neighboring SNPs. You can click the region and sample of interest, and use Up to really zoom in to individual genes (1-10 Mb), while watching the blue copy number curve on the right. Alternatively, use Shift+Up to reduce the SNP height.

 

If Excel cannot display all the data, try Excel 2007 or a text editor.

[simon]

Hi Cheng,

I choose paired normal as reference and  got inferred copy number  , however, some of  normal control are not even close to 2 .  Please see attached output below.
Could you please give me some suggestions?
Thanks
Simon

3.35	3.68	3.22	3.44	3.71	1.93	4.15	4.54
4.05	3.54	5.81	7.75	3.71	1.93	4.15	4.54
4.05	2.64	5.81	7.75	2.72	2.2	4.15	3.08
4.05	3.54	5.81	7.75	3.09	1.93	3.21	3.88

[simon]

Hi Cheng,
I am wondering where can I search snp list for certain gene in dChip?  I only know NCBI could do this.
Thanks
Simon

[Cheng Li]

Simon,

 

You can make a chromosome region file with genes as regions to display SNP in them:

http://biosun1.harvard.edu/complab/dchip/snp_cluster.htm

[simon]

Hi Cheng,
I use paired normal as reference and I choose median smoothing when I do copy number analysis . However, I found big variation of copy number intensity from some normal samples. They are not always close to 2, some even higher than 4 or 5. Could you tell me some reasons?
Thanks
Simon

[simon]

Dear Dr. Li,
Another quick question I have to bother you again is that I try to export the image from chromosome view of copy number, however, sometimes I got  dark blank image. I usually choose export to file and JPG format.I tried all other options but  neither of them work .
Thanks a lot
Simon

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[Cheng Li]

Simon,

 

Probably the image is too large. Try these methods:

http://biosun1.harvard.edu/complab/dchip/clustering.htm#export_image

 

The normal samples with large variation may be due to bad sample quality. You can try to remove them from array list file.

[simon]

Hi Chen,
I am using dChip to analyze affymetrix 6.0 data. I copied all files and generate txt files.  I opened group, select CEL file and import all txt files. There are also JPG ,dcp files in the same folder. I only get excel file ,namely dchip_array_summary file,but  I couldn't get any images files? Could you please help me for that?
Thanks a lot
Simon

--

[Cheng Li]

Simon,

 

To see CEL images by clicking the blue icons on the left, you need to check “Open group/options/load probe data in memory”.

[simon]

Hi Chen,
I am interested in copy number analysis of genes involved in cell cycle regulation. I am wondering is there any way for me to cluster or filter those genes into a group and present the copy number images together which looks similar to the picture in attachment.
Thanks a lot
Simon

[simon]

Hi, Cheng,
I am not sure I made clear of my question last email. I am analyzing copy number alteration with SNP6.0. I want to cluster a couple of interested genes into one image which shows in log2 pattern. I know there are gene expression arrays have done a lot with cluster function.
But, I am wondering COPY NUMBER of individual genes also could use clustering function of dCHIP.
Thanks a lot
Simon

[Cheng Li]

Hi Simon,

 

You may try this function:

 

www.dchip.org/snp_cluster.htm

 

A chromosome region file should be made to contain your interested genes and their chromosome positions (e.g. by copying from refGene file).

[simon]

Hi Cheng and other collegues,
I have a quick question. I am confused with one option in copy number analysis with Chromosome view,  what is the meaning for "# previous snps used " ? I couldn't find any introduction in manual.

Thanks a lot
Simon

[Cheng Li]

Simon,

This option is used only for inferring Major copy proportion, where the dependence of genotypes of neighboring N SNPs in the reference normal samples are computed.

Cheng

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