Quiet Dynamite: XMRV as an Infectious Agent

[dannybex]

Yeah, can someone check Sam and my count? I also got 93.

The subjects in Tables 1 and 2 seem to be the same as those in Table 3 by my spot-checking. I did not check every patient ID number though -- is the remaining 8 from this?

Also, the 75% figure I do not find in the text other than the abstract. If a number is in the abstract, it should also be in the text. Using Table 3, I counted the numbers of people with a positive cDNA PCR test (73) and added to the people with a negative cDNA PCR test but a positive other test (7) ----- with this, I got 80 with a positive test. 80/93 = 86%, not 75%.

Finally, people are right to be confused about the percentages. Back at the CFSAC meeting, they gave out some of this data and from my notes,
there were 33 people negative for PCR but many were positive by some other test. Adding this to the 67 positive PCRs, the number given out was that 99/101= 98% patients tested positive by at least one test. So this is different from the 75% given now as well.

[In addition, the 95% figure was thrown out in relation to antibody testing a few months ago.]

AAARRRRGGHHHHHH....................................someone check the numbers and my logic -- either it's my brain or this paper doesn't make things as clear as they could be.

It's waaaaaay over my head, but I do think these kind of changing percentages doesn't help the WPI. It may not hurt them in the long run, but they need to be consistent...don't they?

 

[SOC]

This journal just got started this year and has an impact factor of about 7, compared to Science's 30. This should have ended up in Science as a reply to early criticisms rather than coming out now.

Just started this year and its impact factor is 7? Makes Retrovirology's impact factor of 4.6 look even more pathetic.

I wonder why it didn't end up in Science, since it is an addendum to that paper. I don't know the etiquette or logistics of that kind of stuff, though. Maybe it's typical to publish an addendum in another journal?

 

[Sam Carter]

Patients 1117, 1120, 1134, 1139,1145,1148,1154,1155,1164,1167,1170,1175,1176 (a total of 13) tested negative, by which I mean they tested negative on all the XMRV tests applied to them.

To find the upper bound of patients in this cohort who tested negative we would assume the missing 8 patients were all negative which would be 13+8=21. This is equivalent to saying that a maximum of (21/101)*100 = 20.79% were XMRV negative.

Therefore, the minimum XMRV positive rate demonstrated by the study is 100-20.79=79.21% not 75% and this assumes all the missing patients are negative.(*)

(*) it also assumes that my maths is correct.......

 

[George]

My dog brain explodes every time I try to do WPI math. (big grins)

I love these guys but I sometimes wonder if they need new calculators.

Or maybe we all just need new brains? I'm up for that!

 

[Hope123]

Just started this year and its impact factor is 7? Makes Retrovirology's impact factor of 4.6 look even more pathetic.

I wonder why it didn't end up in Science, since it is an addendum to that paper. I don't know the etiquette or logistics of that kind of stuff, though. Maybe it's typical to publish an addendum in another journal?

I don't know why. A possibility is space considerations but then I would think they could do an online addendum?

 

[Hope123]

Patients 1117, 1120, 1134, 1139,1145,1148,1154,1155,1164,1167,1170,1175,1176 (a total of 13) tested negative, by which I mean they tested negative on all the XMRV tests applied to them.

To find the upper bound of patients in this cohort who tested negative we would assume the missing 8 patients were all negative which would be 13+8=21. This is equivalent to saying that a maximum of (21/101)*100 = 20.79% were XMRV negative.



Therefore, the minimum XMRV positive rate demonstrated by the study is 100-20.79=79.21% not 75% and this assumes all the missing patients are negative.(*)

(*) it also assumes that my maths is correct.......

Your figure of "13" agrees with mine but just to clarify, some of those subjects negative by PCR did not have any additional tests done per Table 3 as 'NT' refers to 'not tested' rather than a "-" or "+" which is tested and negative/ positive. (e.g. subject 1170 vs. subject 1235 below)

 

[Sam Carter]

Your figure of "13" agrees with mine but just to clarify, some of those subjects negative by PCR did not have any additional tests done per Table 3 as 'NT' refers to 'not tested' rather than a "-" or "+" which is tested and negative/ positive. (e.g. subject 1170 vs. subject 1235 below)

Hi Hope,

I think I took that into consideration in my calculation ... I was trying to establish the maximum number of XMRV negative people in the cohort so I assumed that all the NTs would be negative.

If my sums are correct (usual caveats apply) then the data show that at least 80% of the cohort are XMRV+ .

Sam

 

[ixchelkali]

The isolation of infectious XMRV from prostate cancer patients will be shown for the first time.

Wow. That's big. I'll be interested to hear the details of that.

 

[aruschima]

George,

It is seven a clock in the morning here, a bad night and seemed like a bad morning as well .....
But than i read your doggy post: about all excited and .... on the floor for nothing ...? I am cracking up laughing and cannot stop.

Thanks so much for making us laugh in such depressing times!

Aruschima

Really, stop the math lesson here, who cares one or two more or less. I just wonder : where is the Dynamite ?

P.s. George, you should try and start as a cartoonist , really ......!

 

[George]

I take my job as comic relief very seriously. Honest, really. Can I have a treat now? (grins)

 

[V99]

They said something like over or above 75%.

 

[JT1024]

Hi George!

I second the motion you should be writing for profit (or for the benefit of all of us with ME/CFS and other neuro-immune disorders. You always make me laugh even when I want to cry!

Your gift for writing serious matters with a humorous tone could very well bring ME/CFS and other neuro-immune disorders to the forefront. I don't know your personal circumstances but I suspect it is like most of us, severely limited in "normal" life. Many have talents but are unable to contribute as they would like.

I know I am having tremendous difficulty because I work full time and that is ALL I can basically do. I am barely able to take care of myself. I feel like I lose ground every day yet I have to make sure I can go to work so I can provide for myself.

Sorry I'm too brain dead to continue.... Thanks to George and others who are able to continually put a smile on my face! ~ JT

 

[SOC]

Really, stop the math lesson here, who cares one or two more or less. I just wonder : where is the Dynamite ?

Oh! Not fair! Some of us like the math! And the numbers do matter.

 

[Hope123]

It's waaaaaay over my head, but I do think these kind of changing percentages doesn't help the WPI. It may not hurt them in the long run, but they need to be consistent...don't they?

Exactamundo! If you can't get your numbers straight or explain the discrepancies, this makes other scientists question what other mistakes or sloppiness might be found in your work.

Oh! Not fair! Some of us like the math! And the numbers do matter.

Yup. Who cares? Scientists, healthcare staff, government, patient advocacy groups...............etc. And YOU should too. Inaccurate calculations/ sloppy record keeping = inaccurate scientific conclusions = possibly wrong treatment for patients/ leading other researchers down the wrong path wasting time,money,resources.

I support the WPI and have donated a not small amount to them but this type of work really makes me concerned.

(Some of this discussion should be moved over to the other thread since this one actually concerns another paper.)

 

[Sam Carter]

How many of the 101 patients test positive for XMRV gag sequences by nested PCR?

The original Science paper reports 68 such patients but this has gone up to 73 in Virulence despite the 8 missing patients.

ETA: the WPI need to explain this discrepancy

 

[aruschima]

If the number problem makes you

concerned, wait till i get my dynamite!

 

[aruschima]

Oh and George, doggy treat is on the way, but be prepared, the CDC might intercept and put it on hold !

 

[George]

Oh and George, doggy treat is on the way, but be prepared, the CDC might intercept and put it on hold !

ROFLMTO, HACK the CDC, Release the dog Treats NOW!

 

[aruschima]

Going to bed now with a big smile .
Have a good day to you all and keep that dynamite coming! CDC is going down !

 

[Levi]

Additional research

http://jvi.asm.org/cgi/content/abstract/84/15/7908