I started to use KNIME a couple of weeks ago and found it really great to extract and transform data from microarrays. Also the integration of R functions is extremly useful allowing me to use functions such as quantiles normalisation within the workflow. However, some useful functions/NODES are missing or either restricted to rows or columns.
Headers are not easy to handle. E.g. microarray files usually contain a header and column names are not given in the first row but in one of the following rows. In order to read this files the option “Enable short lines” has to be activated". Unfortunately, many of the fields containing the columns names are replaced by a “?”. I have no ideay nor can I understand why some fields are not converted. E.g. the following row
Block Row Column Name ID X Y
is converted to
Block ? ? Name ID ? ?
Is there any way to prevent replacement of fields by the missing value “?”? This would be very helpful, since then all rows above the header could be removed and the first row could be turned into a column ID.
- Functions restricted to either rows or columns
Some functions are either restricted to nodes for rows or columns which I found very inconvenient, since I have to use the transform NODE as a workaround (.e.g. the META MODE “Iterate list of files” is extending rows only and not columns, an appropriate node such as rowID is not available for columns). Furthermore, the transform NODE is quite time consuming particularly for larger files. Is it not possible to provide some of these NODES for both columns and rows?
- Read files into meta nodes
If several files are read into a meta note (e.g. “Iterate list of files”) it would be very convenient if the names of the files could be read in and used as column or row names suffix. However, I did not find an appropriate function for this.
For many of the availabel nodes I really have now idea of their usage but I guess some of them might be extremely useful. Is it planned to perform a user seminar/workshop that demonstrates the usage of nodes and allow users to discuss their problems? I could imagine, that this might be interesting for many other users.
Thanks in advance for any comment.