Cel File Not Available. Extracting Cel File Information From The Txt File.

Question

[goldenpirnas]

For some of the microarray datasets, CEL file is not available . But TXT file is available . Is there any way through which CEL file information can be extracted from TXT file?

[Sean Davis]

If the information from the .CEL file that you want is in the TXT file, then yes, but TXT files do not generally contain all the information that is in a .CEL file. What is it that you are actually trying to do? Details are likely to be helpful.

[goldenpirnas]

Yes, Some of the TXT file has the CEL file information. But many doesn't have. Is there any scripts or microarray file format conversion tools available to extract CEL file information from TXT file( "TXT file submitted in the supplementary information" )

[Sean Davis]

There is not such a tool since TXT files are not a standard format.

[goldenpirnas]

Since some of the datasets doesn't have CEL file information , which is the prerequisite for normalization . Is there any other way through which this can be handled ? (Considering some other file format for normalizing the data)

[Neilfws]

Sean is trying to get you to tell us what, precisely, your TXT files look like. Can you provide a small sample or a link to an example?

Answer 1

[Istvan Albert]

The binary CEL format is vendor specific binary data format. A text CEL format is a simplified text representation of that binary format. I believe that you cannot convert backwards from a text based CEL to a binary CEL format because the former lacks some information needed in the latter. Usually this is not a problem as the text version will contain all the information that you typically need for data analysis.

If the tool demands that you use a binary CEL then you will have to find the original data (or use a different tool).

Answer 2

[goldenpirnas]

This is how my TXT file looks, www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM740401 (information represents probeset-level data) Suppl file. TXT (pls download and have a look)

Is there any way u can get a information similar to this , http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM308224 (represent probe-level data) Suppl file. TXT (pls download and have a look)

Both are from different sample files, but i wanted a TXT file which is similar (format wise)to that of second TXT file(need a probe- level data and not probeset-level data ).

Please let me know. Thanking you for your time.

[Sean Davis]

Unfortunately, you will need to write to the authors to get data that is not available via GEO.