Hi Rudy, apologies in advance for the length of this email. And yeah, how about them Cards?? Maybe this will be our year........ Here's my take on the ms (more details below): I think it's pretty well done, perhaps some overstatement in the summary. I have several mainly minor comments, none of which is a 'deal-breaker' - ie, it _could_ go pretty much as is, although I do not think that would be ideal. I have made some edits in the .tex file (yes, it's all a bit anal!!): I made a few small grammatical corrections and corrected a number of spelling errors and name consistency (e.g. HuGeneFL throughout; in the ms there were occurrences of HuGeneFl......that type of thing). I also changed " " to `` '' for nice looking quotes. It was easier to fix the .tex file than to explain to the authors what to do!! If you request the authors to make the additional changes I suggest, then I would advise you to have them make the changes directly in the revision I have attached, and, for your own sanity, tell them what you want them to name their new file (e.g. MorrisRev.tex or MorrisFinal.tex, or whatever naming convention you have decided upon). There are some editorial decisions you might wish to make, here are a few I can think of: in this ms, the authors sometimes use the term 'dataset' but other times call it 'data set'. It is better to have it called the same thing throughout the ms (and better still that all chapters use the same convention!). So, choose one and either ask them to fix it or do it yourself (or ask me). Ditto with 'probeset' - I think they always use 1 word, but as I recall in my chapter we used 'probe set'. If chapter consistency is important to you, pick one. Anyway, I'll fix anything you want in mine. Another minor consistency thing - do you want p-value or $p$-value (ie, italicized p)? I am sure that different authors use different conventions, if you want the same look throughout the chapters you should pick one. If this is not important to you, ignore! Another decision regards citations (I don't know if you have already gotten around to this yet). Their bib is hard-coded into the ms; it is better to have the refs in a separate .bib file, then you can include them in any style you want. You just need to specify the bibliographystyle, which you need to specify in a .bst file - there are several available, it might not be too difficult to find one which matches the form the publishers require, assuming they are not able to provide you with one themselves. Anyway, for your convenience, I have made a .bib file for their ms. If you want, I am more than happy (well kind of!) to do this for other ms if the authors are unable to (but please try to get them to do it first!). In addition, they have hard-coded the citations as well, but you may wish for them to be in a different form. Here I would recommend someone (them, me, worst-case scenario you) going through the ms and changing them to \cite{} form (or \citep{} / \citet{} as in the natbib package, which btw I highly recommend)....it might seem like trouble now, but I would be surprised if it did not save you a few future headaches. Anyway, as I said I am happy to help in this regard -- you already have more than enough to do on this (I know that for a fact), and I have achieved some facility having lived through it myself already. Please please please don't hesitate to ask. Really, I do know how hard it can be to get this kind of 'grunge' work done, and how uncomfortable it is to ask someone to do it. But hey, it's _me_..........so ask! Other grunge tasks you might have will be attacked with equal vigor and pleasure :) My remaining comments, which may be passed on to the authors as is or edited by you first to reflect what you really want for them to do. Please strip off my sig if you send to them (not that I'm concerned here about anonymity....) Best, D ps, hope you have been relatively unaffected by the rash of hurricanes -------------------------------------------------------------------------- Comments to Authors (Morris et al.) p.7, last sentence: identified more genes, how do they know it's a benefit? They could presumably be false positives. p.8 - 'various quality control checks' - what are these? In the Michigan set 10/86 ~ 11% of arrays were discarded. This is a substantial proportion of the original set - to what extent could these `poor quality' arrays have been responsible for the original findings? That is, we would like to know that differences in results are due to methodological differences rather than differences in the actual data set analyzed. pdnn - hard to know what its properties are, it's not in affycomp fig 1.2 - This is a poor graphic. should make these plots squares rather than rectangles, and it would be even better to plot the difference vs the average for both quantities to more clearly highlight the differences in the 2 data sets fig 1.3 - again, it would be useful (though not completely necessary) to plot this in a difference vs average configuration as well; also, it would make more sense to me to see partial vs full (rather than the full vs partial which is shown), since in some sense we might think of partial as a fn of full will the book be having color?? Some of the figs use color and if the book has no color they would need to be redone using different line types. In general, the line width of the plots and plot label sizes should be increased for better readability fig 1.6 - the caption does not explain what the 2 colors represent (which curve is red and which black?). The caption might also explain what test the p-value corresponds to. The comparison of correlations with different quantification methods (sec. 1.7.2) is not entirely clear to me - were the methods applied 'out of the box' on the reduced set of probesets? Does 'pdnn' refer to pdnn plus the other preprocessing? Any additional preprocessing done with the other methods? Which dchip method is used (I assume pm only, but I didn't notice it stated anywhere) The authors have done a nice job motivating, implementing and demonstrating their methods; this type of work is clearly necessary as a prelude to being able to combine raw data for analysis. Like them, I also believe that this will prove more sensitive (and therefore ultimately more fruitful) for finding relevant genes. However, the conclusion seems somewhat overstated here. They state that they have demonstrated the benefit of pooling data; in fact, it seems to me that they have stated that pooling data should be beneficial and have shown how it might be done (again, they have done this well). Sorry if I missed it, but it wasn't sufficiently clear to me that their findings represent true (rather than false) positives. Perhaps they could emphasize the literature findings a bit more? Or be more cautious in arriving at the conclusion that the found genes are good (true) ones? In any case, if they do have evidence that the found genes are true it would be beneficial to see that more prominently displayed. If not, they might just state that their method appears to have promise (or something along those lines). Unlike a number of other methods, it is based on fundamentally sound biological principles, obviously something that works in its favor. -------------------------------------------------------------------------- Quoting Rudy Guerra : > D: > > Can you please review this chapter. A one paragraph summary is > sufficient; anything beyond that would be great. Please let me know > if you can do so within a few weeks. > > -- Rudy > > ================================= > > Rudy Guerra > Professor > Jones College Master > > Department of Statistics MS-138, 6100 Main St., Houston, Texas 77005 > Voice: 713.348.5453 Fax: 713.348.5476 Jones College 713.348.6049 > http://www.stat.rice.edu/~rguerra/ > ----- Original Message ----- > From: "Jeffrey Morris" > To: "Rudy Guerra" > Cc: "jeffrey Morris" ; "Keith Baggerly" > ; "Kevin Coombes" ; > ; ; > Sent: Wednesday, March 16, 2005 5:13 PM > Subject: Re: Meta/combining information book: author instructions > > > Rudy, > > Please see the attached files, containing the latex and pdf version of our > chapter, along with postscript files (sent in a subsequent email). > > Please let me know what else you need from us. > > Regards, > > Jeff > > At 06:51 PM 3/7/2005 -0600, you wrote: > > >Book Contributors: > > > >First and foremost, thank you all very much for accepting > >the invitation to contribute to our book. We, and Chapman-Hall, > >are very excited about the project. Meta-analysis and combining > >information is becoming more and more important and we hope the > >book will be a good entry point for those researchers wanting to > >learn about the area. > > > >Each of you is the contact person for your chapter. I will > >forward you information and you, in turn, should contact > >your co-authors. This email accomplishes a few things: > > > >1. Attached is a fairly complete TOC for the book. I am > >waiting for 1 or 2 more responses, but we are just about > >at capacity. The TOC will give you an idea of the topics, > >the authors, and where you fit in the overall picture. If > >you feel you should in a different part please let me know. > > > >2. Attached are several files from Chapman-Hall. The most > >important parts are (a) the latex style file for your chapter, > >given in a zip file, (b) the Contributor Agreement. You will > >soon be contacted by Preethi Cholmondeley from CH who will > >instruct you on the Agreement; please read over it. The other > >files are a Guide to Publishing, which has very helpful information > >on Permission guidelines, manuscript preparation, and style; > >please take the time to read this Guide as it will save us > >much work down the road. > > > >3. Due dates > >Those of you who agreed early on should be submitting your > >chapter by the end of March, and the others by May. > > > >My notes have the following: > >March: Kendziorski, Morris, Lee, Zhao, Ghosh, Goldstein, Etzel > > Lewis, Guerra, Zhang, Kim, Kimmel > >May: the others > > > >If you will be delayed please let me know asap when we can > >expect your paper. CH is expecting a final product around > >July, so David Allsion and I will need to have all the papers > >by the end of May. This is the so-called hard deadline. > > > >4. We do not want to impose a structure on your papers, but > >we will ask that you keep in mind that the book is expected > >to be read by people who wish to "learn" about the ideas, > >approaches, and methods for MA or combining information; > >for example, graduate students or non-statistical investigators > >such as geneticists, clinical researchers, etc. Therefore, it > >would be helpful to be more pedagogical tahn you would be for > >a journal paper. You should also have something to say about > >implementation/software if appropriate. These are the basics. > >The final published paper should be between 15-25 pages, including > >figures,tables, refs. CH has technical help on latex: > >texhelp@crcpress.com > > > > > >That's it for now. Again, thank you very much for your participation. > > > >**What we need from you right away is a final title, author list, > >and complete affiliation information. > >Please send this information to me by the end of this week.** It > >has to go to CH at that point. > > > >Rudy and David > >=========================================== > >Rudy Guerra > >Professor > >Department of Statistics > >Rice University > > > >713.348.5453 > >Homepage: http://www.stat.rice.edu/~rguerra/ > >Statistics: http://www.stat.rice.edu/ > >Biostatistics Program: http://statistics.rice.edu/grad.cfm?doc_id=3262 > > > >---------- Forwarded message ---------- > >Date: Fri, 18 Jun 2004 14:43:53 -0400 > >From: "Cholmondeley, Preethi" > >To: rguerra@rice.edu > >Cc: daliison@uab.edu > >Subject: C522X You book Meta-Analysis and Combining Information in Genetics > > > >Dr. Guerra, > > > > > > > >My name is Preethi Cholmondeley and I am the Project Coordinator assigned > >to your work Meta-Analysis and Combining Information in Genetics. I will > >be your main contact that will facilitate the production process from now > >on, until the book is transmitted to production. I'm happy to be working > >with you on this book. > > > > > > > >As per Rob Calver, this book has contributed chapters and you already have > >our LaTeX style files. However, I wasn't sure if you have the files for a > >contributed book. So I'm attaching them again. Let me know if you are able > >to download them. > > > > > > > >Technical questions regarding LaTeX can be directed to our helpdesk at > >texhelp@crcpress.com > > > > > > > >According to our file, your book is due by 6/30/2005. If at any time in > >the process of manuscript preparation you experience a delay I ask you to > >please inform me immediately so that I can alert your Acquiring Editor as > >well as all other relevant CRC staff. > > > > > > > >I have highlighted some of our key manuscript requirements. I suggest you > >refer to our Author's Guide and Template attached, for more details. > > > > > > > >* Please follow the attached PDF template provided to ensure that > >your book follows sizing specifications. If you can not open this > >template, please let me know and I will be happy to send you one via > >regular mail. > > > > > > > >* Submit camera ready pages single spaced, left and right margins > >justified, with running heads and folios, on 8 ½ x 11-inch (or A4) paper. > >Also enclose a computer disk or CD-ROM containing the application files > >and fonts used for this initial submission of your book. Include a printed > >directory of the disk or CD-ROM contents showing file names and versions. > > > > > > > >* Submit a full set of front matter with your camera ready pages. > >Front matter should include a preface, editor biographical information, a > >list of all contributors with affiliations and a complete table of > >contents. > > > > > > > >* Provide a signed Contributor Agreement (attached) for each > >contributor. > > > > > > > >* Provide a completed Permission Verification form (attached). This > >form is necessary even if your work does not require permission because it > >is either original or in the public domain. If this is the case, please > >check off Box "A" and sign the form where indicated. Otherwise, list the > >materials that need permission in a particular chapter and the source. > >Whenever possible, original art for which you own the copyright or which > >has never been published before should be provided for your book. When it > >is not possible to provide original artwork, you must secure written > >permission for all previously published figures, even if these figures are > >your own. Securing permission and payment of any fees is the > >responsibility of each editor, author, and contributor. Written permission > >must include all rights (as defined in your contract, including electronic > >rights) and must accompany the initial submission of your pages. If > >permission cannot be secured for all rights, replace the figure, table, > >etc. with original art. If you have any questions about permissions or > >need help finding copyright holders contact details, please contact me and > >I will assist you. > > > > > > > >In addition, we ask that you please submit two sample chapters of your > >works early in the preparation process (usually about 4 months before the > >manuscript is due in). Please include all fonts used and electronic > >files, both text and art, for these chapters. This will allow us to > >evaluate your samples and make suggestions. A reminder will be sent out to > >you nearer the time. > > > > > > > >I would be extremely grateful if we could start the process off by asking > >you to send the Contributor Agreement attached to this email to each > >contributor. They can sign the agreement and directly forward it to me. I > >would also be grateful if you could please send me a list of contributors > >to me via email. > > > > > > > >I look forward to hearing from you shortly. > > > > > > > >Best regards, > > > > > > > >Preethi. > > > > > > > > > > > >Preethi Cholmondeley > > > >Project Coordinator > > > >CRC Press > > > >2000 NW Corporate Blvd. > > > >Boca Raton, FL 33431 > > > >Tel: (561) 998-2511 > > > >Fax: (561) 997-7249 > > > >Email: pcholmondeley@crcpress.com > > > > > > > > > > > > -------------------------------------------------------------------------------- > > > > > -- Darlene Goldstein École Polytechnique Fédérale de Lausanne (EPFL) Institut de mathématiques Bâtiment MA, Station 8 Tel: +41 21 693 2552 CH-1015 Lausanne Fax: +41 21 693 4303 SWITZERLAND