CEL files have the same time tag

[Cheng Li]

Thu Jul 20, 2006 5:00 pm
Hi Jai,

In the latest dchip, you can uncheck "Open group/options/Check CEL
file time
tag", if you are sure that these two files are for different samples.

Cheng


From: Jai Prakash Mehta [mailto:jai.m...@mail.dcu.ie]
Sent: Thursday, July 20, 2006 6:01 AM
To: dc...@yahoogroups.com
Subject: Have the same time tag

Hi All,

Any one has any comments on this error/warning message "Have the same
time tag [03/07/03 13:56:17] as 'G:\additional public datasets
\pawitan
breast samples\cel\b chip\GSM107374.CEL', ignored"

It comes during the experiment uploading process.

Thanks in advance

Jai Prakash Mehta



Posted: 17 Jul 2007 11:47 am Post subject: How to analyze data with
No Time Tag?

--------------------------------------------------------------------------------

Thu Dec 22, 2005 7:30 pm
Hi Anna,

Please use the updated dchip:
Http://biosun1.harvard.edu/~cli/dchip2006.exe

Uncheck "Open group/options/check cel file time tag". When you open
the
group for the 2nd time, only checking "Open group/DCP file".

Thanks

Cheng


From: annat [mailto:an...@breastcenter.tmc.edu]
Sent: Monday, December 19, 2005 10:23 AM
To: cli; dchip
Cc: annat
Subject: How to analyze data with No Time Tag?

Dear Cheng, dear developers and users,
I received data for U133AAofAv2 chip.
The experiments have been run in another institution.
When I am trying to run dChip, the message says that all the chips
have
same time tag [No Tag], and only the very first chip is taken for
analysis. I found in the past that this dChip feature is very useful.
But is there a way to bypass this to analyze the data this time? I
would
highly appreciate your help. I realise that it is Holidays and
vacation
time. Happy Holidays and New year. Anna Tsimelzon



Mon May 16, 2005 5:35 pm

dChip considers the CEL, DAT or DCP files with the same time tag (can
be
found in the header line of CEL file) as identical files and only read
in
one of the identical files. If CEL files of two different samples
happen to
have the same time tag, one may change the time tag manually in one of
the
CEL file header (open CEL file in a text editor), e.g: change ?01/18/
1
13:43:17? to ?01/18/ 1 13:43:18?.

Cheng


From: dc...@yahoogroups.com [mailto:dc...@yahoogroups.com]On Behalf
Of
Tracy, Sean I.
Sent: Monday, May 16, 2005 5:16 PM
To: dc...@yahoogroups.com
Subject: [dchip]

Hi,
Dchip refuses to open a .dcp file because it has the "same time tag
[no
time]" as another, unrelated .dcp array file. Any suggestions on how
to fix
this?

ST



Thu Jan 30, 2003 10:24 pm
Thomas,

The time stamps are obtained from CEL file headers (you may open a CEL
file by text editor). You may change the time stamp a little in one
file to get around this problem. But if these two CEL files are
identical for many rows (say 1000), probably they are the same file.

Cheng


From: Thomas <tcw...@hotmail.com> [mailto:tcw...@hotmail.com]
Sent: Thursday, January 30, 2003 9:16 PM
To: dc...@yahoogroups.com
Subject: [dchip] Time Tag Restrictions

Hello All,
Inputting a large number of files into the software (75 received from
an outside source w/o the accompanying CHP, EXP, RPT, etc. files), I
ran into the following error on four of the files:
"Found C:\Tom\GeneLogic\94458hgu95a11.cel
Have the same time tag [10/12/ 1 12:27:07]
as 'C:\Tom\GeneLogic\94422hgu95a11.cel', ignored"
Two things:
1) Looking at the two files through windows explorer, these two files
have the same date but different time stamps (as viewed through the
CEL file's properties window). In addition, these times and dates
are both different from that reported in dChip.
2) When looking at the CEL files in MAS 5.0, I could make out no
information in the CEL file other than the actual scaled picture
(i.e. there was no internal date/time stamp).
I would obviously like to get around this problem and generate my
numbers. BTW, I tried this same CEL file set with 1.1, 1.2, and 1.3
with the same results.

I would appreciate any light that could be shed on this subject.

Thank You,
Thomas Whisenant
DNA Microarray Core Facility
The Scripps Research Institute



Mon Aug 8, 2005 1:11 pm
Erez,

dChip considers the CEL, DAT or DCP files with the same time tag (can
be
found in the header line of CEL file) as identical files and only read
in
one of the identical files. If CEL files of two different samples
happen to
have the same time tag, one may change the time tag manually in one of
the
CEL file header (open CEL file in a text editor), e.g: change ?01/18/
1
13:43:17? to ?01/18/ 1 13:43:18?.

Cheng


From: dc...@yahoogroups.com [mailto:dc...@yahoogroups.com]On Behalf
Of
erez_feige
Sent: Monday, August 08, 2005 1:07 PM
To: dc...@yahoogroups.com
Subject: [dchip] U133AAofAv2

Hi I'm trying to compare gene expression data from U133AAofAv2 high
throughput arrays. I have multiple CEL results files, and using the
correct CDF file from Affymetrix, I try to open and analyze them
using
dChip.
However, while opening the group, I get an error message saying :
Found filename.CEL > Have the same time tag [No time] as
filename2.CEL, ignored, and eventually, after background calculation,
I get `Treat all the 1 arrays as 1 samples and 1 sample groups`, all
the CEL files are summed up to one grid-like array. Since multiple
samples are considered as one, I cannot compare them.
Any suggestions? Can anyone refer me to a suitable gene info file?

Thanks,
Erez.



Wed Aug 23, 2006 10:10 pm
Hi Sanchita,

Thanks for reporting the issue.

You can try to uncheck "Open group/options/Check CEL file time tag".

Cheng


From: not...@yahoogroups.com [mailto:not...@yahoogroups.com] On Behalf
Of
sanchita_c
Sent: Wednesday, August 23, 2006 6:54 PM
Subject: Affy High Throughput arrays

Hi Cheng,

I loaded 64 .cel files from the Affy High Throughput Human arrays
into
the latest version of dchip. I found out that only first .cel file
from the given set is read by the dchip rest are ignored. I have
attached the error message for better understanding.

The hight throught put Human arrays are different from the single
Hgu133A chips. The cdf file is HT_Hgu133A since the coordinates are
totally different.

I will realy appreciate if you can help me in troubleshooting the
error message I am getting.

Error message:

Welcome to dChip 2006 (DNA-Chip Analyzer), Build date: Jul 18 2006
Select 'Help/Website' for manual and updates

This is a dChip version with internal file format 4. It can be used
for 500K SNP array and exon array analysis. If you use it to analyze
previous dChip data, CDF or CEL files will be re-extracted

08/23/06, 15:44

{Open group dChip
Read in existing binary CDF file C:\Program
Files\Stratagene\ArrayAssist 3\Library\HT_HG-U133A.cdf.bin (file
format 4)...

Search and extract PM/MM data from 'CEL' files of chip type
'HT_HG-U133A' in
C:\Documents and Settings\Sanchita\My Documents\NSCOR\test...

Found C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.CEL
Accessing 'C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.dcp' (file format 4)
Found C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A02.CEL
Have the same time tag [No time] as 'C:\Documents and
Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.CEL', ignored
Found C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A03.CEL
Have the same time tag [No time] as 'C:\Documents and
Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.CEL', ignored
Found C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A04.CEL
Have the same time tag [No time] as 'C:\Documents and
Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.CEL', ignored
Found C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A05.CEL
Have the same time tag [No time] as 'C:\Documents and
Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.CEL', ignored
Found C:\Documents and Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A06.CEL
Have the same time tag [No time] as 'C:\Documents and
Settings\Sanchita\My
Documents\NSCOR\test\5500024016257061106711.A01.CEL', ignored

Writing array summary file C:\Documents and Settings\Sanchita\My
Documents\DTRA-DOEset\dchip\dChip arrays.xls

Group "dChip" contains 1 arrays; see 'C:\Documents and
Settings\Sanchita\My Documents\DTRA-DOEset\dchip\dChip arrays.xls'
for
details

Treat all the 1 arrays as 1 samples and 1 sample groups



Posted: 30 Jun 2008 04:18 pm Post subject: same time tag always =
identical file?

--------------------------------------------------------------------------------

Hi, my name is Sophia. I am an undergraduate student at WashU working
on a microarray project over the summer. I understand that this topic
has already been asked, but I am wondering when two files have the
same time tag, does this necessarily mean that they are the same file?
I am analyzing data which I procured from multiple sources (GEOdataset
and from some lab I know), and from my analysis, I am suspecting that
two files were mis labeled. I am making this judgement because not
only because of the error message but also because the gene list do
not include some specific cell markers.

Also, a second question I have is that when the expression of one gene
on an array AFTER normalization is 1, does this indicate there is
almost no expression of the gene on that array? Does it display 1
because it is the lowest expression possible after normalization?

There is unfortunately no one else in my lab who uses dChip. Any help
would be appreciated. Thank you



Posted: 01 Jul 2008 01:55 pm Post subject:

--------------------------------------------------------------------------------

Hi Sophia,

Welcome to the forum.

You can open two CEL files in text editors and compare their headers
(first 100 lines). If the headers are identical, the files are most
likely the same. If in doubt you can post them here.

1 is a truncated value and ususally means both PM and MM probes are
close to the background, and the gene is absent in the sample or
expressed at an undetectable level.

Cheng